| Previous changeset 22:3d0c7bdf12f5 (2021-09-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 9aa395df821f0d3607867c83536ac97f9ffe8b29 |
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modified:
rgFastQC.xml test-data/fastqc_data.txt test-data/fastqc_data_adapters.txt test-data/fastqc_data_contaminants.txt test-data/fastqc_data_customlimits.txt test-data/fastqc_data_hisat.txt test-data/fastqc_data_kmer.txt test-data/fastqc_data_min_length.txt test-data/fastqc_data_nogroup.txt test-data/fastqc_report.html test-data/fastqc_report_adapters.html test-data/fastqc_report_contaminants.html test-data/fastqc_report_customlimits.html test-data/fastqc_report_hisat.html test-data/fastqc_report_kmer.html test-data/fastqc_report_min_length.html test-data/fastqc_report_nogroup.html |
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| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee rgFastQC.xml --- a/rgFastQC.xml Sun Sep 12 11:20:27 2021 +0000 +++ b/rgFastQC.xml Thu Jun 08 20:02:11 2023 +0000 |
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| @@ -1,10 +1,10 @@ -<tool id="fastqc" name="FastQC" version="0.73+galaxy0"> +<tool id="fastqc" name="FastQC" version="0.74+galaxy0"> <description>Read Quality reports</description> <xrefs> <xref type="bio.tools">fastqc</xref> </xrefs> <requirements> - <requirement type="package" version="0.11.9">fastqc</requirement> + <requirement type="package" version="0.12.1">fastqc</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="FastQC returned non zero exit code" /> |
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| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_data.txt --- a/test-data/fastqc_data.txt Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_data.txt Thu Jun 08 20:02:11 2023 +0000 |
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| @@ -1,10 +1,11 @@ -##FastQC 0.11.9 +##FastQC 0.12.1 >>Basic Statistics pass #Measure Value Filename 1000trimmed_fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4905 +Total Bases 254.2 kbp Sequences flagged as poor quality 0 Sequence length 1-108 %GC 40 @@ -344,81 +345,81 @@ >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.73598369011212 -#Duplication Level Percentage of deduplicated Percentage of total -1 99.44249432170142 98.1855249745158 -2 0.47491224447656405 0.9378185524974516 -3 0.041296716911005574 0.12232415902140673 -4 0.020648358455502787 0.08154943934760449 -5 0.0 0.0 -6 0.0 0.0 -7 0.0 0.0 -8 0.0 0.0 -9 0.0 0.0 ->10 0.020648358455502787 0.672782874617737 ->50 0.0 0.0 ->100 0.0 0.0 ->500 0.0 0.0 ->1k 0.0 0.0 ->5k 0.0 0.0 ->10k+ 0.0 0.0 +#Duplication Level Percentage of total +1 98.1855249745158 +2 0.9378185524974516 +3 0.12232415902140673 +4 0.08154943934760449 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +>10 0.672782874617737 +>50 0.0 +>100 0.0 +>500 0.0 +>1k 0.0 +>5k 0.0 +>10k+ 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT 33 0.672782874617737 No Hit >>END_MODULE >>Adapter Content pass -#Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter -1 0.0 0.0 0.0 0.0 0.0 -2 0.0 0.0 0.0 0.0 0.0 -3 0.0 0.0 0.0 0.0 0.0 -4 0.0 0.0 0.0 0.0 0.0 -5 0.0 0.0 0.0 0.0 0.0 -6 0.0 0.0 0.0 0.0 0.0 -7 0.0 0.0 0.0 0.0 0.0 -8 0.0 0.0 0.0 0.0 0.0 -9 0.0 0.0 0.0 0.0 0.0 -10-11 0.0 0.0 0.0 0.0 0.0 -12-13 0.0 0.0 0.0 0.0 0.0 -14-15 0.0 0.0 0.0 0.0 0.0 -16-17 0.0 0.0 0.0 0.0 0.0 -18-19 0.0 0.0 0.0 0.0 0.0 -20-21 0.12232415902140673 0.0 0.0 0.0 0.0 -22-23 0.12232415902140673 0.0 0.0 0.0 0.0 -24-25 0.12232415902140673 0.0 0.0 0.0 0.0 -26-27 0.1325178389398573 0.0 0.0 0.0 0.0 -28-29 0.2038735983690112 0.0 0.0 0.0 0.0 -30-31 0.22426095820591233 0.0 0.0 0.0 0.0 -32-33 0.22426095820591233 0.0 0.0 0.0 0.0 -34-35 0.24464831804281345 0.0 0.0 0.0 0.0 -36-37 0.3058103975535168 0.0 0.0 0.0 0.0 -38-39 0.4383282364933741 0.0 0.0 0.0 0.0 -40-41 0.4689092762487258 0.0 0.0 0.0 0.0 -42-43 0.4689092762487258 0.0 0.0 0.0 0.0 -44-45 0.4689092762487258 0.0 0.0 0.0 0.0 -46-47 0.4689092762487258 0.0 0.0 0.0 0.0 -48-49 0.4689092762487258 0.0 0.0 0.0 0.0 -50-51 0.4689092762487258 0.0 0.0 0.0 0.0 -52-53 0.4689092762487258 0.0 0.0 0.0 0.0 -54-55 0.4689092762487258 0.0 0.0 0.0 0.0 -56-57 0.4689092762487258 0.0 0.0 0.0 0.0 -58-59 0.4689092762487258 0.0 0.0 0.0 0.0 -60-61 0.4689092762487258 0.0 0.0 0.0 0.0 -62-63 0.4689092762487258 0.0 0.0 0.0 0.0 -64-65 0.4689092762487258 0.0 0.0 0.0 0.0 -66-67 0.4689092762487258 0.0 0.0 0.0 0.0 -68-69 0.4689092762487258 0.0 0.0 0.0 0.0 -70-71 0.4689092762487258 0.0 0.0 0.0 0.0 -72-73 0.4689092762487258 0.0 0.0 0.0 0.0 -74-75 0.4689092762487258 0.0 0.0 0.0 0.0 -76-77 0.4689092762487258 0.0 0.0 0.0 0.0 -78-79 0.4689092762487258 0.0 0.0 0.0 0.0 -80-81 0.4689092762487258 0.0 0.0 0.0 0.0 -82-83 0.4689092762487258 0.0 0.0 0.0 0.0 -84-85 0.4689092762487258 0.0 0.0 0.0 0.0 -86-87 0.4689092762487258 0.0 0.0 0.0 0.0 -88-89 0.4689092762487258 0.0 0.0 0.0 0.0 -90-91 0.4689092762487258 0.0 0.0 0.0 0.0 -92-93 0.4689092762487258 0.0 0.0 0.0 0.0 -94-95 0.4689092762487258 0.0 0.0 0.0 0.0 -96-97 0.4689092762487258 0.0 0.0 0.0 0.0 +#Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence PolyA PolyG +1 0.0 0.0 0.0 0.0 0.020387359836901122 0.0 +2 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +3 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +4 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +5 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +6 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +7 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +8 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +9 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +10-11 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +12-13 0.0 0.0 0.0 0.0 0.1529051987767584 0.0 +14-15 0.0 0.0 0.0 0.0 0.17329255861365955 0.0 +16-17 0.0 0.0 0.0 0.0 0.21406727828746175 0.0 +18-19 0.0 0.0 0.0 0.0 0.22426095820591233 0.0 +20-21 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +22-23 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +24-25 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +26-27 0.1325178389398573 0.0 0.0 0.0 0.24464831804281345 0.0 +28-29 0.2038735983690112 0.0 0.0 0.0 0.24464831804281345 0.0 +30-31 0.22426095820591233 0.0 0.0 0.0 0.24464831804281345 0.0 +32-33 0.22426095820591233 0.0 0.0 0.0 0.2650356778797146 0.0 +34-35 0.24464831804281345 0.0 0.0 0.0 0.29561671763506625 0.0 +36-37 0.3058103975535168 0.0 0.0 0.0 0.31600407747196735 0.0 +38-39 0.4383282364933741 0.0 0.0 0.0 0.32619775739041795 0.0 +40-41 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +42-43 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +44-45 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +46-47 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +48-49 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +50-51 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +52-53 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +54-55 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +56-57 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +58-59 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +60-61 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +62-63 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +64-65 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +66-67 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +68-69 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +70-71 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +72-73 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +74-75 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +76-77 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +78-79 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +80-81 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +82-83 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +84-85 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +86-87 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +88-89 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +90-91 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +92-93 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +94-95 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +96-97 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 >>END_MODULE |
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| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_data_adapters.txt --- a/test-data/fastqc_data_adapters.txt Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_data_adapters.txt Thu Jun 08 20:02:11 2023 +0000 |
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| @@ -1,10 +1,11 @@ -##FastQC 0.11.9 +##FastQC 0.12.1 >>Basic Statistics pass #Measure Value Filename 1000trimmed_fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4905 +Total Bases 254.2 kbp Sequences flagged as poor quality 0 Sequence length 1-108 %GC 40 @@ -344,23 +345,23 @@ >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.73598369011212 -#Duplication Level Percentage of deduplicated Percentage of total -1 99.44249432170142 98.1855249745158 -2 0.47491224447656405 0.9378185524974516 -3 0.041296716911005574 0.12232415902140673 -4 0.020648358455502787 0.08154943934760449 -5 0.0 0.0 -6 0.0 0.0 -7 0.0 0.0 -8 0.0 0.0 -9 0.0 0.0 ->10 0.020648358455502787 0.672782874617737 ->50 0.0 0.0 ->100 0.0 0.0 ->500 0.0 0.0 ->1k 0.0 0.0 ->5k 0.0 0.0 ->10k+ 0.0 0.0 +#Duplication Level Percentage of total +1 98.1855249745158 +2 0.9378185524974516 +3 0.12232415902140673 +4 0.08154943934760449 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +>10 0.672782874617737 +>50 0.0 +>100 0.0 +>500 0.0 +>1k 0.0 +>5k 0.0 +>10k+ 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source |
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| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_data_contaminants.txt --- a/test-data/fastqc_data_contaminants.txt Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_data_contaminants.txt Thu Jun 08 20:02:11 2023 +0000 |
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| @@ -1,10 +1,11 @@ -##FastQC 0.11.9 +##FastQC 0.12.1 >>Basic Statistics pass #Measure Value Filename 1000trimmed_fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4905 +Total Bases 254.2 kbp Sequences flagged as poor quality 0 Sequence length 1-108 %GC 40 @@ -344,81 +345,81 @@ >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.73598369011212 -#Duplication Level Percentage of deduplicated Percentage of total -1 99.44249432170142 98.1855249745158 -2 0.47491224447656405 0.9378185524974516 -3 0.041296716911005574 0.12232415902140673 -4 0.020648358455502787 0.08154943934760449 -5 0.0 0.0 -6 0.0 0.0 -7 0.0 0.0 -8 0.0 0.0 -9 0.0 0.0 ->10 0.020648358455502787 0.672782874617737 ->50 0.0 0.0 ->100 0.0 0.0 ->500 0.0 0.0 ->1k 0.0 0.0 ->5k 0.0 0.0 ->10k+ 0.0 0.0 +#Duplication Level Percentage of total +1 98.1855249745158 +2 0.9378185524974516 +3 0.12232415902140673 +4 0.08154943934760449 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +>10 0.672782874617737 +>50 0.0 +>100 0.0 +>500 0.0 +>1k 0.0 +>5k 0.0 +>10k+ 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT 33 0.672782874617737 TestContaminant (100% over 24bp) >>END_MODULE >>Adapter Content pass -#Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter -1 0.0 0.0 0.0 0.0 0.0 -2 0.0 0.0 0.0 0.0 0.0 -3 0.0 0.0 0.0 0.0 0.0 -4 0.0 0.0 0.0 0.0 0.0 -5 0.0 0.0 0.0 0.0 0.0 -6 0.0 0.0 0.0 0.0 0.0 -7 0.0 0.0 0.0 0.0 0.0 -8 0.0 0.0 0.0 0.0 0.0 -9 0.0 0.0 0.0 0.0 0.0 -10-11 0.0 0.0 0.0 0.0 0.0 -12-13 0.0 0.0 0.0 0.0 0.0 -14-15 0.0 0.0 0.0 0.0 0.0 -16-17 0.0 0.0 0.0 0.0 0.0 -18-19 0.0 0.0 0.0 0.0 0.0 -20-21 0.12232415902140673 0.0 0.0 0.0 0.0 -22-23 0.12232415902140673 0.0 0.0 0.0 0.0 -24-25 0.12232415902140673 0.0 0.0 0.0 0.0 -26-27 0.1325178389398573 0.0 0.0 0.0 0.0 -28-29 0.2038735983690112 0.0 0.0 0.0 0.0 -30-31 0.22426095820591233 0.0 0.0 0.0 0.0 -32-33 0.22426095820591233 0.0 0.0 0.0 0.0 -34-35 0.24464831804281345 0.0 0.0 0.0 0.0 -36-37 0.3058103975535168 0.0 0.0 0.0 0.0 -38-39 0.4383282364933741 0.0 0.0 0.0 0.0 -40-41 0.4689092762487258 0.0 0.0 0.0 0.0 -42-43 0.4689092762487258 0.0 0.0 0.0 0.0 -44-45 0.4689092762487258 0.0 0.0 0.0 0.0 -46-47 0.4689092762487258 0.0 0.0 0.0 0.0 -48-49 0.4689092762487258 0.0 0.0 0.0 0.0 -50-51 0.4689092762487258 0.0 0.0 0.0 0.0 -52-53 0.4689092762487258 0.0 0.0 0.0 0.0 -54-55 0.4689092762487258 0.0 0.0 0.0 0.0 -56-57 0.4689092762487258 0.0 0.0 0.0 0.0 -58-59 0.4689092762487258 0.0 0.0 0.0 0.0 -60-61 0.4689092762487258 0.0 0.0 0.0 0.0 -62-63 0.4689092762487258 0.0 0.0 0.0 0.0 -64-65 0.4689092762487258 0.0 0.0 0.0 0.0 -66-67 0.4689092762487258 0.0 0.0 0.0 0.0 -68-69 0.4689092762487258 0.0 0.0 0.0 0.0 -70-71 0.4689092762487258 0.0 0.0 0.0 0.0 -72-73 0.4689092762487258 0.0 0.0 0.0 0.0 -74-75 0.4689092762487258 0.0 0.0 0.0 0.0 -76-77 0.4689092762487258 0.0 0.0 0.0 0.0 -78-79 0.4689092762487258 0.0 0.0 0.0 0.0 -80-81 0.4689092762487258 0.0 0.0 0.0 0.0 -82-83 0.4689092762487258 0.0 0.0 0.0 0.0 -84-85 0.4689092762487258 0.0 0.0 0.0 0.0 -86-87 0.4689092762487258 0.0 0.0 0.0 0.0 -88-89 0.4689092762487258 0.0 0.0 0.0 0.0 -90-91 0.4689092762487258 0.0 0.0 0.0 0.0 -92-93 0.4689092762487258 0.0 0.0 0.0 0.0 -94-95 0.4689092762487258 0.0 0.0 0.0 0.0 -96-97 0.4689092762487258 0.0 0.0 0.0 0.0 +#Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence PolyA PolyG +1 0.0 0.0 0.0 0.0 0.020387359836901122 0.0 +2 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +3 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +4 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +5 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +6 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +7 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +8 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +9 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +10-11 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +12-13 0.0 0.0 0.0 0.0 0.1529051987767584 0.0 +14-15 0.0 0.0 0.0 0.0 0.17329255861365955 0.0 +16-17 0.0 0.0 0.0 0.0 0.21406727828746175 0.0 +18-19 0.0 0.0 0.0 0.0 0.22426095820591233 0.0 +20-21 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +22-23 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +24-25 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +26-27 0.1325178389398573 0.0 0.0 0.0 0.24464831804281345 0.0 +28-29 0.2038735983690112 0.0 0.0 0.0 0.24464831804281345 0.0 +30-31 0.22426095820591233 0.0 0.0 0.0 0.24464831804281345 0.0 +32-33 0.22426095820591233 0.0 0.0 0.0 0.2650356778797146 0.0 +34-35 0.24464831804281345 0.0 0.0 0.0 0.29561671763506625 0.0 +36-37 0.3058103975535168 0.0 0.0 0.0 0.31600407747196735 0.0 +38-39 0.4383282364933741 0.0 0.0 0.0 0.32619775739041795 0.0 +40-41 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +42-43 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +44-45 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +46-47 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +48-49 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +50-51 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +52-53 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +54-55 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +56-57 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +58-59 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +60-61 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +62-63 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +64-65 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +66-67 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +68-69 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +70-71 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +72-73 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +74-75 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +76-77 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +78-79 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +80-81 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +82-83 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +84-85 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +86-87 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +88-89 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +90-91 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +92-93 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +94-95 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +96-97 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 >>END_MODULE |
| b |
| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_data_customlimits.txt --- a/test-data/fastqc_data_customlimits.txt Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_data_customlimits.txt Thu Jun 08 20:02:11 2023 +0000 |
| b |
| @@ -1,10 +1,11 @@ -##FastQC 0.11.9 +##FastQC 0.12.1 >>Basic Statistics pass #Measure Value Filename 1000trimmed_fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4905 +Total Bases 254.2 kbp Sequences flagged as poor quality 0 Sequence length 1-108 %GC 40 @@ -344,83 +345,83 @@ >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.73598369011212 -#Duplication Level Percentage of deduplicated Percentage of total -1 99.44249432170142 98.1855249745158 -2 0.47491224447656405 0.9378185524974516 -3 0.041296716911005574 0.12232415902140673 -4 0.020648358455502787 0.08154943934760449 -5 0.0 0.0 -6 0.0 0.0 -7 0.0 0.0 -8 0.0 0.0 -9 0.0 0.0 ->10 0.020648358455502787 0.672782874617737 ->50 0.0 0.0 ->100 0.0 0.0 ->500 0.0 0.0 ->1k 0.0 0.0 ->5k 0.0 0.0 ->10k+ 0.0 0.0 +#Duplication Level Percentage of total +1 98.1855249745158 +2 0.9378185524974516 +3 0.12232415902140673 +4 0.08154943934760449 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +>10 0.672782874617737 +>50 0.0 +>100 0.0 +>500 0.0 +>1k 0.0 +>5k 0.0 +>10k+ 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT 33 0.672782874617737 No Hit >>END_MODULE >>Adapter Content pass -#Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter -1 0.0 0.0 0.0 0.0 0.0 -2 0.0 0.0 0.0 0.0 0.0 -3 0.0 0.0 0.0 0.0 0.0 -4 0.0 0.0 0.0 0.0 0.0 -5 0.0 0.0 0.0 0.0 0.0 -6 0.0 0.0 0.0 0.0 0.0 -7 0.0 0.0 0.0 0.0 0.0 -8 0.0 0.0 0.0 0.0 0.0 -9 0.0 0.0 0.0 0.0 0.0 -10-11 0.0 0.0 0.0 0.0 0.0 -12-13 0.0 0.0 0.0 0.0 0.0 -14-15 0.0 0.0 0.0 0.0 0.0 -16-17 0.0 0.0 0.0 0.0 0.0 -18-19 0.0 0.0 0.0 0.0 0.0 -20-21 0.12232415902140673 0.0 0.0 0.0 0.0 -22-23 0.12232415902140673 0.0 0.0 0.0 0.0 -24-25 0.12232415902140673 0.0 0.0 0.0 0.0 -26-27 0.1325178389398573 0.0 0.0 0.0 0.0 -28-29 0.2038735983690112 0.0 0.0 0.0 0.0 -30-31 0.22426095820591233 0.0 0.0 0.0 0.0 -32-33 0.22426095820591233 0.0 0.0 0.0 0.0 -34-35 0.24464831804281345 0.0 0.0 0.0 0.0 -36-37 0.3058103975535168 0.0 0.0 0.0 0.0 -38-39 0.4383282364933741 0.0 0.0 0.0 0.0 -40-41 0.4689092762487258 0.0 0.0 0.0 0.0 -42-43 0.4689092762487258 0.0 0.0 0.0 0.0 -44-45 0.4689092762487258 0.0 0.0 0.0 0.0 -46-47 0.4689092762487258 0.0 0.0 0.0 0.0 -48-49 0.4689092762487258 0.0 0.0 0.0 0.0 -50-51 0.4689092762487258 0.0 0.0 0.0 0.0 -52-53 0.4689092762487258 0.0 0.0 0.0 0.0 -54-55 0.4689092762487258 0.0 0.0 0.0 0.0 -56-57 0.4689092762487258 0.0 0.0 0.0 0.0 -58-59 0.4689092762487258 0.0 0.0 0.0 0.0 -60-61 0.4689092762487258 0.0 0.0 0.0 0.0 -62-63 0.4689092762487258 0.0 0.0 0.0 0.0 -64-65 0.4689092762487258 0.0 0.0 0.0 0.0 -66-67 0.4689092762487258 0.0 0.0 0.0 0.0 -68-69 0.4689092762487258 0.0 0.0 0.0 0.0 -70-71 0.4689092762487258 0.0 0.0 0.0 0.0 -72-73 0.4689092762487258 0.0 0.0 0.0 0.0 -74-75 0.4689092762487258 0.0 0.0 0.0 0.0 -76-77 0.4689092762487258 0.0 0.0 0.0 0.0 -78-79 0.4689092762487258 0.0 0.0 0.0 0.0 -80-81 0.4689092762487258 0.0 0.0 0.0 0.0 -82-83 0.4689092762487258 0.0 0.0 0.0 0.0 -84-85 0.4689092762487258 0.0 0.0 0.0 0.0 -86-87 0.4689092762487258 0.0 0.0 0.0 0.0 -88-89 0.4689092762487258 0.0 0.0 0.0 0.0 -90-91 0.4689092762487258 0.0 0.0 0.0 0.0 -92-93 0.4689092762487258 0.0 0.0 0.0 0.0 -94-95 0.4689092762487258 0.0 0.0 0.0 0.0 -96-97 0.4689092762487258 0.0 0.0 0.0 0.0 +#Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence PolyA PolyG +1 0.0 0.0 0.0 0.0 0.020387359836901122 0.0 +2 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +3 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +4 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +5 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +6 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +7 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +8 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +9 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +10-11 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +12-13 0.0 0.0 0.0 0.0 0.1529051987767584 0.0 +14-15 0.0 0.0 0.0 0.0 0.17329255861365955 0.0 +16-17 0.0 0.0 0.0 0.0 0.21406727828746175 0.0 +18-19 0.0 0.0 0.0 0.0 0.22426095820591233 0.0 +20-21 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +22-23 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +24-25 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +26-27 0.1325178389398573 0.0 0.0 0.0 0.24464831804281345 0.0 +28-29 0.2038735983690112 0.0 0.0 0.0 0.24464831804281345 0.0 +30-31 0.22426095820591233 0.0 0.0 0.0 0.24464831804281345 0.0 +32-33 0.22426095820591233 0.0 0.0 0.0 0.2650356778797146 0.0 +34-35 0.24464831804281345 0.0 0.0 0.0 0.29561671763506625 0.0 +36-37 0.3058103975535168 0.0 0.0 0.0 0.31600407747196735 0.0 +38-39 0.4383282364933741 0.0 0.0 0.0 0.32619775739041795 0.0 +40-41 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +42-43 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +44-45 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +46-47 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +48-49 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +50-51 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +52-53 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +54-55 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +56-57 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +58-59 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +60-61 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +62-63 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +64-65 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +66-67 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +68-69 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +70-71 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +72-73 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +74-75 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +76-77 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +78-79 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +80-81 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +82-83 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +84-85 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +86-87 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +88-89 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +90-91 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +92-93 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +94-95 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +96-97 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE |
| b |
| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_data_hisat.txt --- a/test-data/fastqc_data_hisat.txt Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_data_hisat.txt Thu Jun 08 20:02:11 2023 +0000 |
| b |
| @@ -1,10 +1,11 @@ -##FastQC 0.11.9 +##FastQC 0.12.1 >>Basic Statistics pass #Measure Value Filename hisat_output_1_bam File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 20 +Total Bases 1.4 kbp Sequences flagged as poor quality 0 Sequence length 70 %GC 43 @@ -342,106 +343,106 @@ >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 100.0 -#Duplication Level Percentage of deduplicated Percentage of total -1 100.0 100.0 -2 0.0 0.0 -3 0.0 0.0 -4 0.0 0.0 -5 0.0 0.0 -6 0.0 0.0 -7 0.0 0.0 -8 0.0 0.0 -9 0.0 0.0 ->10 0.0 0.0 ->50 0.0 0.0 ->100 0.0 0.0 ->500 0.0 0.0 ->1k 0.0 0.0 ->5k 0.0 0.0 ->10k+ 0.0 0.0 +#Duplication Level Percentage of total +1 100.0 +2 0.0 +3 0.0 +4 0.0 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +>10 0.0 +>50 0.0 +>100 0.0 +>500 0.0 +>1k 0.0 +>5k 0.0 +>10k+ 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source -GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTC 1 5.0 No Hit -CCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCT 1 5.0 No Hit -TAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTCAAGCGCCGAGGATGCGTGACCGT 1 5.0 No Hit -CTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCA 1 5.0 No Hit -CTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAA 1 5.0 No Hit -TCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTCATTTCATTGATTTGGTCATT 1 5.0 No Hit -GCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACATAGTGC 1 5.0 No Hit -CTGAATGGAATTAAGAAAACCACCAATACCAGCATTAACCTTCAAACTATCAAAATATAACGTTGACGAT 1 5.0 No Hit -CTCAAATCCGGCGTCAACCATACCAGCATAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAATCTCA 1 5.0 No Hit -CAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGCTAGAA 1 5.0 No Hit -GTGAAATTTCTAGGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCA 1 5.0 No Hit -TGTTTTCCGTAAATTCAGCGCCTTCCATGATGCGACAGGCCGTTTGAATGTTGACGGGATGAACATAATA 1 5.0 No Hit -CCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCT 1 5.0 No Hit -TGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTT 1 5.0 No Hit -GCGACCATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCGACGAAGACTCAAAGCGA 1 5.0 No Hit -TTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATTACTACTGCTTGTTTACGAAT 1 5.0 No Hit -TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAG 1 5.0 No Hit -CTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAAAT 1 5.0 No Hit -ACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCAATCCAAACTTTGTTACTC 1 5.0 No Hit -TTAGGTGTGTGTAAAACAGGTGCCGAAGAAGCTGGATTAACAGAATTGAGAACCAGCTTATCAGAAAAAA 1 5.0 No Hit +CCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAG 1 5.0 No Hit +TGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTA 1 5.0 No Hit +ACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAG 1 5.0 No Hit +TGTTTTCCGTAAATTCAGCGCCTTCCATGATGCGACAGGCCGTTTGAATG 1 5.0 No Hit +CTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT 1 5.0 No Hit +TCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTC 1 5.0 No Hit +CCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTT 1 5.0 No Hit +TAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTCAAG 1 5.0 No Hit +CAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAG 1 5.0 No Hit +GCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAG 1 5.0 No Hit +CTGAATGGAATTAAGAAAACCACCAATACCAGCATTAACCTTCAAACTAT 1 5.0 No Hit +GCGACCATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAA 1 5.0 No Hit +GTGAAATTTCTAGGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAG 1 5.0 No Hit +CTCAAATCCGGCGTCAACCATACCAGCATAGGAAGCATCAGCACCAGCAC 1 5.0 No Hit +TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACC 1 5.0 No Hit +CTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATA 1 5.0 No Hit +TTAGGTGTGTGTAAAACAGGTGCCGAAGAAGCTGGATTAACAGAATTGAG 1 5.0 No Hit +GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGA 1 5.0 No Hit +TTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATT 1 5.0 No Hit +CTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAA 1 5.0 No Hit >>END_MODULE >>Adapter Content pass -#Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter -1 0.0 0.0 0.0 0.0 0.0 -2 0.0 0.0 0.0 0.0 0.0 -3 0.0 0.0 0.0 0.0 0.0 -4 0.0 0.0 0.0 0.0 0.0 -5 0.0 0.0 0.0 0.0 0.0 -6 0.0 0.0 0.0 0.0 0.0 -7 0.0 0.0 0.0 0.0 0.0 -8 0.0 0.0 0.0 0.0 0.0 -9 0.0 0.0 0.0 0.0 0.0 -10 0.0 0.0 0.0 0.0 0.0 -11 0.0 0.0 0.0 0.0 0.0 -12 0.0 0.0 0.0 0.0 0.0 -13 0.0 0.0 0.0 0.0 0.0 -14 0.0 0.0 0.0 0.0 0.0 -15 0.0 0.0 0.0 0.0 0.0 -16 0.0 0.0 0.0 0.0 0.0 -17 0.0 0.0 0.0 0.0 0.0 -18 0.0 0.0 0.0 0.0 0.0 -19 0.0 0.0 0.0 0.0 0.0 -20 0.0 0.0 0.0 0.0 0.0 -21 0.0 0.0 0.0 0.0 0.0 -22 0.0 0.0 0.0 0.0 0.0 -23 0.0 0.0 0.0 0.0 0.0 -24 0.0 0.0 0.0 0.0 0.0 -25 0.0 0.0 0.0 0.0 0.0 -26 0.0 0.0 0.0 0.0 0.0 -27 0.0 0.0 0.0 0.0 0.0 -28 0.0 0.0 0.0 0.0 0.0 -29 0.0 0.0 0.0 0.0 0.0 -30 0.0 0.0 0.0 0.0 0.0 -31 0.0 0.0 0.0 0.0 0.0 -32 0.0 0.0 0.0 0.0 0.0 -33 0.0 0.0 0.0 0.0 0.0 -34 0.0 0.0 0.0 0.0 0.0 -35 0.0 0.0 0.0 0.0 0.0 -36 0.0 0.0 0.0 0.0 0.0 -37 0.0 0.0 0.0 0.0 0.0 -38 0.0 0.0 0.0 0.0 0.0 -39 0.0 0.0 0.0 0.0 0.0 -40 0.0 0.0 0.0 0.0 0.0 -41 0.0 0.0 0.0 0.0 0.0 -42 0.0 0.0 0.0 0.0 0.0 -43 0.0 0.0 0.0 0.0 0.0 -44 0.0 0.0 0.0 0.0 0.0 -45 0.0 0.0 0.0 0.0 0.0 -46 0.0 0.0 0.0 0.0 0.0 -47 0.0 0.0 0.0 0.0 0.0 -48 0.0 0.0 0.0 0.0 0.0 -49 0.0 0.0 0.0 0.0 0.0 -50 0.0 0.0 0.0 0.0 0.0 -51 0.0 0.0 0.0 0.0 0.0 -52 0.0 0.0 0.0 0.0 0.0 -53 0.0 0.0 0.0 0.0 0.0 -54 0.0 0.0 0.0 0.0 0.0 -55 0.0 0.0 0.0 0.0 0.0 -56 0.0 0.0 0.0 0.0 0.0 -57 0.0 0.0 0.0 0.0 0.0 -58 0.0 0.0 0.0 0.0 0.0 -59 0.0 0.0 0.0 0.0 0.0 +#Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence PolyA PolyG +1 0.0 0.0 0.0 0.0 0.0 0.0 +2 0.0 0.0 0.0 0.0 0.0 0.0 +3 0.0 0.0 0.0 0.0 0.0 0.0 +4 0.0 0.0 0.0 0.0 0.0 0.0 +5 0.0 0.0 0.0 0.0 0.0 0.0 +6 0.0 0.0 0.0 0.0 0.0 0.0 +7 0.0 0.0 0.0 0.0 0.0 0.0 +8 0.0 0.0 0.0 0.0 0.0 0.0 +9 0.0 0.0 0.0 0.0 0.0 0.0 +10 0.0 0.0 0.0 0.0 0.0 0.0 +11 0.0 0.0 0.0 0.0 0.0 0.0 +12 0.0 0.0 0.0 0.0 0.0 0.0 +13 0.0 0.0 0.0 0.0 0.0 0.0 +14 0.0 0.0 0.0 0.0 0.0 0.0 +15 0.0 0.0 0.0 0.0 0.0 0.0 +16 0.0 0.0 0.0 0.0 0.0 0.0 +17 0.0 0.0 0.0 0.0 0.0 0.0 +18 0.0 0.0 0.0 0.0 0.0 0.0 +19 0.0 0.0 0.0 0.0 0.0 0.0 +20 0.0 0.0 0.0 0.0 0.0 0.0 +21 0.0 0.0 0.0 0.0 0.0 0.0 +22 0.0 0.0 0.0 0.0 0.0 0.0 +23 0.0 0.0 0.0 0.0 0.0 0.0 +24 0.0 0.0 0.0 0.0 0.0 0.0 +25 0.0 0.0 0.0 0.0 0.0 0.0 +26 0.0 0.0 0.0 0.0 0.0 0.0 +27 0.0 0.0 0.0 0.0 0.0 0.0 +28 0.0 0.0 0.0 0.0 0.0 0.0 +29 0.0 0.0 0.0 0.0 0.0 0.0 +30 0.0 0.0 0.0 0.0 0.0 0.0 +31 0.0 0.0 0.0 0.0 0.0 0.0 +32 0.0 0.0 0.0 0.0 0.0 0.0 +33 0.0 0.0 0.0 0.0 0.0 0.0 +34 0.0 0.0 0.0 0.0 0.0 0.0 +35 0.0 0.0 0.0 0.0 0.0 0.0 +36 0.0 0.0 0.0 0.0 0.0 0.0 +37 0.0 0.0 0.0 0.0 0.0 0.0 +38 0.0 0.0 0.0 0.0 0.0 0.0 +39 0.0 0.0 0.0 0.0 0.0 0.0 +40 0.0 0.0 0.0 0.0 0.0 0.0 +41 0.0 0.0 0.0 0.0 0.0 0.0 +42 0.0 0.0 0.0 0.0 0.0 0.0 +43 0.0 0.0 0.0 0.0 0.0 0.0 +44 0.0 0.0 0.0 0.0 0.0 0.0 +45 0.0 0.0 0.0 0.0 0.0 0.0 +46 0.0 0.0 0.0 0.0 0.0 0.0 +47 0.0 0.0 0.0 0.0 0.0 0.0 +48 0.0 0.0 0.0 0.0 0.0 0.0 +49 0.0 0.0 0.0 0.0 0.0 0.0 +50 0.0 0.0 0.0 0.0 0.0 0.0 +51 0.0 0.0 0.0 0.0 0.0 0.0 +52 0.0 0.0 0.0 0.0 0.0 0.0 +53 0.0 0.0 0.0 0.0 0.0 0.0 +54 0.0 0.0 0.0 0.0 0.0 0.0 +55 0.0 0.0 0.0 0.0 0.0 0.0 +56 0.0 0.0 0.0 0.0 0.0 0.0 +57 0.0 0.0 0.0 0.0 0.0 0.0 +58 0.0 0.0 0.0 0.0 0.0 0.0 +59 0.0 0.0 0.0 0.0 0.0 0.0 >>END_MODULE |
| b |
| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_data_kmer.txt --- a/test-data/fastqc_data_kmer.txt Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_data_kmer.txt Thu Jun 08 20:02:11 2023 +0000 |
| b |
| @@ -1,10 +1,11 @@ -##FastQC 0.11.9 +##FastQC 0.12.1 >>Basic Statistics pass #Measure Value Filename 1000trimmed_fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4905 +Total Bases 254.2 kbp Sequences flagged as poor quality 0 Sequence length 1-108 %GC 40 @@ -344,83 +345,83 @@ >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.73598369011212 -#Duplication Level Percentage of deduplicated Percentage of total -1 99.44249432170142 98.1855249745158 -2 0.47491224447656405 0.9378185524974516 -3 0.041296716911005574 0.12232415902140673 -4 0.020648358455502787 0.08154943934760449 -5 0.0 0.0 -6 0.0 0.0 -7 0.0 0.0 -8 0.0 0.0 -9 0.0 0.0 ->10 0.020648358455502787 0.672782874617737 ->50 0.0 0.0 ->100 0.0 0.0 ->500 0.0 0.0 ->1k 0.0 0.0 ->5k 0.0 0.0 ->10k+ 0.0 0.0 +#Duplication Level Percentage of total +1 98.1855249745158 +2 0.9378185524974516 +3 0.12232415902140673 +4 0.08154943934760449 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +>10 0.672782874617737 +>50 0.0 +>100 0.0 +>500 0.0 +>1k 0.0 +>5k 0.0 +>10k+ 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT 33 0.672782874617737 No Hit >>END_MODULE >>Adapter Content pass -#Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter -1 0.0 0.0 0.0 0.0 0.0 -2 0.0 0.0 0.0 0.0 0.0 -3 0.0 0.0 0.0 0.0 0.0 -4 0.0 0.0 0.0 0.0 0.0 -5 0.0 0.0 0.0 0.0 0.0 -6 0.0 0.0 0.0 0.0 0.0 -7 0.0 0.0 0.0 0.0 0.0 -8 0.0 0.0 0.0 0.0 0.0 -9 0.0 0.0 0.0 0.0 0.0 -10-11 0.0 0.0 0.0 0.0 0.0 -12-13 0.0 0.0 0.0 0.0 0.0 -14-15 0.0 0.0 0.0 0.0 0.0 -16-17 0.0 0.0 0.0 0.0 0.0 -18-19 0.0 0.0 0.0 0.0 0.0 -20-21 0.12232415902140673 0.0 0.0 0.0 0.0 -22-23 0.12232415902140673 0.0 0.0 0.0 0.0 -24-25 0.12232415902140673 0.0 0.0 0.0 0.0 -26-27 0.1325178389398573 0.0 0.0 0.0 0.0 -28-29 0.2038735983690112 0.0 0.0 0.0 0.0 -30-31 0.22426095820591233 0.0 0.0 0.0 0.0 -32-33 0.22426095820591233 0.0 0.0 0.0 0.0 -34-35 0.24464831804281345 0.0 0.0 0.0 0.0 -36-37 0.3058103975535168 0.0 0.0 0.0 0.0 -38-39 0.4383282364933741 0.0 0.0 0.0 0.0 -40-41 0.4689092762487258 0.0 0.0 0.0 0.0 -42-43 0.4689092762487258 0.0 0.0 0.0 0.0 -44-45 0.4689092762487258 0.0 0.0 0.0 0.0 -46-47 0.4689092762487258 0.0 0.0 0.0 0.0 -48-49 0.4689092762487258 0.0 0.0 0.0 0.0 -50-51 0.4689092762487258 0.0 0.0 0.0 0.0 -52-53 0.4689092762487258 0.0 0.0 0.0 0.0 -54-55 0.4689092762487258 0.0 0.0 0.0 0.0 -56-57 0.4689092762487258 0.0 0.0 0.0 0.0 -58-59 0.4689092762487258 0.0 0.0 0.0 0.0 -60-61 0.4689092762487258 0.0 0.0 0.0 0.0 -62-63 0.4689092762487258 0.0 0.0 0.0 0.0 -64-65 0.4689092762487258 0.0 0.0 0.0 0.0 -66-67 0.4689092762487258 0.0 0.0 0.0 0.0 -68-69 0.4689092762487258 0.0 0.0 0.0 0.0 -70-71 0.4689092762487258 0.0 0.0 0.0 0.0 -72-73 0.4689092762487258 0.0 0.0 0.0 0.0 -74-75 0.4689092762487258 0.0 0.0 0.0 0.0 -76-77 0.4689092762487258 0.0 0.0 0.0 0.0 -78-79 0.4689092762487258 0.0 0.0 0.0 0.0 -80-81 0.4689092762487258 0.0 0.0 0.0 0.0 -82-83 0.4689092762487258 0.0 0.0 0.0 0.0 -84-85 0.4689092762487258 0.0 0.0 0.0 0.0 -86-87 0.4689092762487258 0.0 0.0 0.0 0.0 -88-89 0.4689092762487258 0.0 0.0 0.0 0.0 -90-91 0.4689092762487258 0.0 0.0 0.0 0.0 -92-93 0.4689092762487258 0.0 0.0 0.0 0.0 -94-95 0.4689092762487258 0.0 0.0 0.0 0.0 -96-97 0.4689092762487258 0.0 0.0 0.0 0.0 +#Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence PolyA PolyG +1 0.0 0.0 0.0 0.0 0.020387359836901122 0.0 +2 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +3 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +4 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +5 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +6 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +7 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +8 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +9 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +10-11 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +12-13 0.0 0.0 0.0 0.0 0.1529051987767584 0.0 +14-15 0.0 0.0 0.0 0.0 0.17329255861365955 0.0 +16-17 0.0 0.0 0.0 0.0 0.21406727828746175 0.0 +18-19 0.0 0.0 0.0 0.0 0.22426095820591233 0.0 +20-21 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +22-23 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +24-25 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +26-27 0.1325178389398573 0.0 0.0 0.0 0.24464831804281345 0.0 +28-29 0.2038735983690112 0.0 0.0 0.0 0.24464831804281345 0.0 +30-31 0.22426095820591233 0.0 0.0 0.0 0.24464831804281345 0.0 +32-33 0.22426095820591233 0.0 0.0 0.0 0.2650356778797146 0.0 +34-35 0.24464831804281345 0.0 0.0 0.0 0.29561671763506625 0.0 +36-37 0.3058103975535168 0.0 0.0 0.0 0.31600407747196735 0.0 +38-39 0.4383282364933741 0.0 0.0 0.0 0.32619775739041795 0.0 +40-41 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +42-43 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +44-45 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +46-47 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +48-49 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +50-51 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +52-53 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +54-55 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +56-57 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +58-59 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +60-61 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +62-63 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +64-65 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +66-67 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +68-69 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +70-71 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +72-73 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +74-75 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +76-77 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +78-79 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +80-81 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +82-83 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +84-85 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +86-87 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +88-89 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +90-91 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +92-93 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +94-95 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +96-97 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position |
| b |
| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_data_min_length.txt --- a/test-data/fastqc_data_min_length.txt Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_data_min_length.txt Thu Jun 08 20:02:11 2023 +0000 |
| b |
| @@ -1,10 +1,11 @@ -##FastQC 0.11.9 +##FastQC 0.12.1 >>Basic Statistics pass #Measure Value Filename 1000trimmed_fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4905 +Total Bases 254.2 kbp Sequences flagged as poor quality 0 Sequence length 1-108 %GC 40 @@ -344,87 +345,87 @@ >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.73598369011212 -#Duplication Level Percentage of deduplicated Percentage of total -1 99.44249432170142 98.1855249745158 -2 0.47491224447656405 0.9378185524974516 -3 0.041296716911005574 0.12232415902140673 -4 0.020648358455502787 0.08154943934760449 -5 0.0 0.0 -6 0.0 0.0 -7 0.0 0.0 -8 0.0 0.0 -9 0.0 0.0 ->10 0.020648358455502787 0.672782874617737 ->50 0.0 0.0 ->100 0.0 0.0 ->500 0.0 0.0 ->1k 0.0 0.0 ->5k 0.0 0.0 ->10k+ 0.0 0.0 +#Duplication Level Percentage of total +1 98.1855249745158 +2 0.9378185524974516 +3 0.12232415902140673 +4 0.08154943934760449 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +>10 0.672782874617737 +>50 0.0 +>100 0.0 +>500 0.0 +>1k 0.0 +>5k 0.0 +>10k+ 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT 33 0.672782874617737 No Hit >>END_MODULE >>Adapter Content pass -#Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter -1 0.0 0.0 0.0 0.0 0.0 -2 0.0 0.0 0.0 0.0 0.0 -3 0.0 0.0 0.0 0.0 0.0 -4 0.0 0.0 0.0 0.0 0.0 -5 0.0 0.0 0.0 0.0 0.0 -6 0.0 0.0 0.0 0.0 0.0 -7 0.0 0.0 0.0 0.0 0.0 -8 0.0 0.0 0.0 0.0 0.0 -9 0.0 0.0 0.0 0.0 0.0 -10-11 0.0 0.0 0.0 0.0 0.0 -12-13 0.0 0.0 0.0 0.0 0.0 -14-15 0.0 0.0 0.0 0.0 0.0 -16-17 0.0 0.0 0.0 0.0 0.0 -18-19 0.0 0.0 0.0 0.0 0.0 -20-21 0.12232415902140673 0.0 0.0 0.0 0.0 -22-23 0.12232415902140673 0.0 0.0 0.0 0.0 -24-25 0.12232415902140673 0.0 0.0 0.0 0.0 -26-27 0.1325178389398573 0.0 0.0 0.0 0.0 -28-29 0.2038735983690112 0.0 0.0 0.0 0.0 -30-31 0.22426095820591233 0.0 0.0 0.0 0.0 -32-33 0.22426095820591233 0.0 0.0 0.0 0.0 -34-35 0.24464831804281345 0.0 0.0 0.0 0.0 -36-37 0.3058103975535168 0.0 0.0 0.0 0.0 -38-39 0.4383282364933741 0.0 0.0 0.0 0.0 -40-41 0.4689092762487258 0.0 0.0 0.0 0.0 -42-43 0.4689092762487258 0.0 0.0 0.0 0.0 -44-45 0.4689092762487258 0.0 0.0 0.0 0.0 -46-47 0.4689092762487258 0.0 0.0 0.0 0.0 -48-49 0.4689092762487258 0.0 0.0 0.0 0.0 -50-51 0.4689092762487258 0.0 0.0 0.0 0.0 -52-53 0.4689092762487258 0.0 0.0 0.0 0.0 -54-55 0.4689092762487258 0.0 0.0 0.0 0.0 -56-57 0.4689092762487258 0.0 0.0 0.0 0.0 -58-59 0.4689092762487258 0.0 0.0 0.0 0.0 -60-61 0.4689092762487258 0.0 0.0 0.0 0.0 -62-63 0.4689092762487258 0.0 0.0 0.0 0.0 -64-65 0.4689092762487258 0.0 0.0 0.0 0.0 -66-67 0.4689092762487258 0.0 0.0 0.0 0.0 -68-69 0.4689092762487258 0.0 0.0 0.0 0.0 -70-71 0.4689092762487258 0.0 0.0 0.0 0.0 -72-73 0.4689092762487258 0.0 0.0 0.0 0.0 -74-75 0.4689092762487258 0.0 0.0 0.0 0.0 -76-77 0.4689092762487258 0.0 0.0 0.0 0.0 -78-79 0.4689092762487258 0.0 0.0 0.0 0.0 -80-81 0.4689092762487258 0.0 0.0 0.0 0.0 -82-83 0.4689092762487258 0.0 0.0 0.0 0.0 -84-85 0.4689092762487258 0.0 0.0 0.0 0.0 -86-87 0.4689092762487258 0.0 0.0 0.0 0.0 -88-89 0.4689092762487258 0.0 0.0 0.0 0.0 -90-91 0.4689092762487258 0.0 0.0 0.0 0.0 -92-93 0.4689092762487258 0.0 0.0 0.0 0.0 -94-95 0.4689092762487258 0.0 0.0 0.0 0.0 -96-97 0.4689092762487258 0.0 0.0 0.0 0.0 -98-99 0.0 0.0 0.0 0.0 0.0 -100-101 0.0 0.0 0.0 0.0 0.0 -102-103 0.0 0.0 0.0 0.0 0.0 -104-105 0.0 0.0 0.0 0.0 0.0 -106-107 0.0 0.0 0.0 0.0 0.0 -108 0.0 0.0 0.0 0.0 0.0 +#Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence PolyA PolyG +1 0.0 0.0 0.0 0.0 0.020387359836901122 0.0 +2 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +3 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +4 0.0 0.0 0.0 0.0 0.06116207951070336 0.0 +5 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +6 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +7 0.0 0.0 0.0 0.0 0.12232415902140673 0.0 +8 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +9 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +10-11 0.0 0.0 0.0 0.0 0.14271151885830785 0.0 +12-13 0.0 0.0 0.0 0.0 0.1529051987767584 0.0 +14-15 0.0 0.0 0.0 0.0 0.17329255861365955 0.0 +16-17 0.0 0.0 0.0 0.0 0.21406727828746175 0.0 +18-19 0.0 0.0 0.0 0.0 0.22426095820591233 0.0 +20-21 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +22-23 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +24-25 0.12232415902140673 0.0 0.0 0.0 0.24464831804281345 0.0 +26-27 0.1325178389398573 0.0 0.0 0.0 0.24464831804281345 0.0 +28-29 0.2038735983690112 0.0 0.0 0.0 0.24464831804281345 0.0 +30-31 0.22426095820591233 0.0 0.0 0.0 0.24464831804281345 0.0 +32-33 0.22426095820591233 0.0 0.0 0.0 0.2650356778797146 0.0 +34-35 0.24464831804281345 0.0 0.0 0.0 0.29561671763506625 0.0 +36-37 0.3058103975535168 0.0 0.0 0.0 0.31600407747196735 0.0 +38-39 0.4383282364933741 0.0 0.0 0.0 0.32619775739041795 0.0 +40-41 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +42-43 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +44-45 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +46-47 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +48-49 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +50-51 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +52-53 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +54-55 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +56-57 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +58-59 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +60-61 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +62-63 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +64-65 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +66-67 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +68-69 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +70-71 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +72-73 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +74-75 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +76-77 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +78-79 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +80-81 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +82-83 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +84-85 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +86-87 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +88-89 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +90-91 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +92-93 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +94-95 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +96-97 0.4689092762487258 0.0 0.0 0.0 0.32619775739041795 0.0 +98-99 0.0 0.0 0.0 0.0 0.0 0.0 +100-101 0.0 0.0 0.0 0.0 0.0 0.0 +102-103 0.0 0.0 0.0 0.0 0.0 0.0 +104-105 0.0 0.0 0.0 0.0 0.0 0.0 +106-107 0.0 0.0 0.0 0.0 0.0 0.0 +108 0.0 0.0 0.0 0.0 0.0 0.0 >>END_MODULE |
| b |
| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_data_nogroup.txt --- a/test-data/fastqc_data_nogroup.txt Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_data_nogroup.txt Thu Jun 08 20:02:11 2023 +0000 |
| b |
| b"@@ -1,10 +1,11 @@\n-##FastQC\t0.11.9\n+##FastQC\t0.12.1\n >>Basic Statistics\tpass\n #Measure\tValue\n Filename\t1000trimmed_fastq\n File type\tConventional base calls\n Encoding\tSanger / Illumina 1.9\n Total Sequences\t4905\n+Total Bases\t254.2 kbp\n Sequences flagged as poor quality\t0\n Sequence length\t1-108\n %GC\t40\n@@ -577,125 +578,125 @@\n >>END_MODULE\n >>Sequence Duplication Levels\tpass\n #Total Deduplicated Percentage\t98.73598369011212\n-#Duplication Level\tPercentage of deduplicated\tPercentage of total\n-1\t99.44249432170142\t98.1855249745158\n-2\t0.47491224447656405\t0.9378185524974516\n-3\t0.041296716911005574\t0.12232415902140673\n-4\t0.020648358455502787\t0.08154943934760449\n-5\t0.0\t0.0\n-6\t0.0\t0.0\n-7\t0.0\t0.0\n-8\t0.0\t0.0\n-9\t0.0\t0.0\n->10\t0.020648358455502787\t0.672782874617737\n->50\t0.0\t0.0\n->100\t0.0\t0.0\n->500\t0.0\t0.0\n->1k\t0.0\t0.0\n->5k\t0.0\t0.0\n->10k+\t0.0\t0.0\n+#Duplication Level\tPercentage of total\n+1\t98.1855249745158\n+2\t0.9378185524974516\n+3\t0.12232415902140673\n+4\t0.08154943934760449\n+5\t0.0\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+>10\t0.672782874617737\n+>50\t0.0\n+>100\t0.0\n+>500\t0.0\n+>1k\t0.0\n+>5k\t0.0\n+>10k+\t0.0\n >>END_MODULE\n >>Overrepresented sequences\twarn\n #Sequence\tCount\tPercentage\tPossible Source\n ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\t33\t0.672782874617737\tNo Hit\n >>END_MODULE\n >>Adapter Content\tpass\n-#Position\tIllumina Universal Adapter\tIllumina Small RNA 3' Adapter\tIllumina Small RNA 5' Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n-1\t0.0\t0.0\t0.0\t0.0\t0.0\n-2\t0.0\t0.0\t0.0\t0.0\t0.0\n-3\t0.0\t0.0\t0.0\t0.0\t0.0\n-4\t0.0\t0.0\t0.0\t0.0\t0.0\n-5\t0.0\t0.0\t0.0\t0.0\t0.0\n-6\t0.0\t0.0\t0.0\t0.0\t0.0\n-7\t0.0\t0.0\t0.0\t0.0\t0.0\n-8\t0.0\t0.0\t0.0\t0.0\t0.0\n-9\t0.0\t0.0\t0.0\t0.0\t0.0\n-10\t0.0\t0.0\t0.0\t0.0\t0.0\n-11\t0.0\t0.0\t0.0\t0.0\t0.0\n-12\t0.0\t0.0\t0.0\t0.0\t0.0\n-13\t0.0\t0.0\t0.0\t0.0\t0.0\n-14\t0.0\t0.0\t0.0\t0.0\t0.0\n-15\t0.0\t0.0\t0.0\t0.0\t0.0\n-16\t0.0\t0.0\t0.0\t0.0\t0.0\n-17\t0.0\t0.0\t0.0\t0.0\t0.0\n-18\t0.0\t0.0\t0.0\t0.0\t0.0\n-19\t0.0\t0.0\t0.0\t0.0\t0.0\n-20\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n-21\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n-22\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n-23\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n-24\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n-25\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n-26\t0.12232415902140673\t0.0\t0.0\t0.0\t0.0\n-27\t0.14271151885830785\t0.0\t0.0\t0.0\t0.0\n-28\t0.1834862385321101\t0.0\t0.0\t0.0\t0.0\n-29\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n-30\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n-31\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n-32\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n-33\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n-34\t0.22426095820591233\t0.0\t0.0\t0.0\t0.0\n-35\t0.2650356778797146\t0.0\t0.0\t0.0\t0.0\n-36\t0.2854230377166157\t0.0\t0.0\t0.0\t0.0\n-37\t0.32619775739041795\t0.0\t0.0\t0.0\t0.0\n-38\t0.4077471967380224\t0.0\t0.0\t0.0\t0.0\n-39\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-40\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-41\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-42\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-43\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-44\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-45\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-46\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-47\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-48\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-49\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-50\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-51\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-52\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-53\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-54\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-55\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-56\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-57\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-58\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-59\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-60\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-61\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-62\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-63\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-64\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-65\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-66\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-67\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-68\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-69\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-70\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-71\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-72\t0.4689092762487258\t0.0\t0.0\t0.0\t0.0\n-73\t0.4689092762487258\t0"..b'.0\t0.0\t0.24464831804281345\t0.0\n+31\t0.22426095820591233\t0.0\t0.0\t0.0\t0.24464831804281345\t0.0\n+32\t0.22426095820591233\t0.0\t0.0\t0.0\t0.24464831804281345\t0.0\n+33\t0.22426095820591233\t0.0\t0.0\t0.0\t0.2854230377166157\t0.0\n+34\t0.22426095820591233\t0.0\t0.0\t0.0\t0.2854230377166157\t0.0\n+35\t0.2650356778797146\t0.0\t0.0\t0.0\t0.3058103975535168\t0.0\n+36\t0.2854230377166157\t0.0\t0.0\t0.0\t0.3058103975535168\t0.0\n+37\t0.32619775739041795\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+38\t0.4077471967380224\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+39\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+40\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+41\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+42\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+43\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+44\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+45\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+46\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+47\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+48\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+49\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+50\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+51\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+52\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+53\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+54\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+55\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+56\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+57\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+58\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+59\t0.4689092762487258\t0.0\t0.0\t0.0\t0.32619775739041795\t0.0\n+60\t0.4689092762487258\t0.0\t0.0\t0.0\t0.3261977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>>END_MODULE\n' |
| b |
| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_report.html --- a/test-data/fastqc_report.html Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_report.html Thu Jun 08 20:02:11 2023 +0000 |
| b |
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alt="Adapter graph"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.12.1)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_report_adapters.html --- a/test-data/fastqc_report_adapters.html Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_report_adapters.html Thu Jun 08 20:02:11 2023 +0000 |
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alt="Adapter graph"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.12.1)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_report_contaminants.html --- a/test-data/fastqc_report_contaminants.html Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_report_contaminants.html Thu Jun 08 20:02:11 2023 +0000 |
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alt="Adapter graph"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.12.1)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_report_customlimits.html --- a/test-data/fastqc_report_customlimits.html Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_report_customlimits.html Thu Jun 08 20:02:11 2023 +0000 |
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alt="Adapter graph"/></p></div><div class="module"><h2 id="M11"><img src="data:image/png;base64,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" alt="[OK]"/>Kmer Content</h2><p>No overrepresented Kmers</p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.12.1)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_report_hisat.html --- a/test-data/fastqc_report_hisat.html Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_report_hisat.html Thu Jun 08 20:02:11 2023 +0000 |
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alt="Adapter graph"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.12.1)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_report_kmer.html --- a/test-data/fastqc_report_kmer.html Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_report_kmer.html Thu Jun 08 20:02:11 2023 +0000 |
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alt="Kmer graph"/></p><table><thead><tr><th>Sequence</th><th>Count</th><th>PValue</th><th>Obs/Exp Max</th><th>Max Obs/Exp Position</th></tr></thead><tbody><tr><td>ACG</td><td>80</td><td>0.0068203025</td><td>21.952587</td><td>94-95</td></tr><tr><td>TAT</td><td>565</td><td>1.3306382E-4</td><td>9.658028</td><td>104-105</td></tr></tbody></table></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.12.1)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_report_min_length.html --- a/test-data/fastqc_report_min_length.html Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_report_min_length.html Thu Jun 08 20:02:11 2023 +0000 |
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alt="Adapter graph"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.12.1)</div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 3d0c7bdf12f5 -r 5ec9f6bceaee test-data/fastqc_report_nogroup.html --- a/test-data/fastqc_report_nogroup.html Sun Sep 12 11:20:27 2021 +0000 +++ b/test-data/fastqc_report_nogroup.html Thu Jun 08 20:02:11 2023 +0000 |
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alt="Adapter graph"/></p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.12.1)</div></body></html>\n\\ No newline at end of file\n' |