+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
70: TopHat on data 1, data 4, and data 3: accepted_hits
70.8%
0.3
75: TopHat on data 1, data 6, and data 5: accepted_hits
69.6%
0.4
80: TopHat on data 1, data 8, and data 7: accepted_hits
71.8%
0.4
85: TopHat on data 1, data 10, and data 9: accepted_hits
72.0%
0.4
90: TopHat on data 1, data 12, and data 11: accepted_hits
71.3%
0.4
95: TopHat on data 1, data 14, and data 13: accepted_hits
70.7%
0.5
bismark_data
0.2
69.7%
dataset_114
0.6%
dataset_197
176bp
272bp
dataset_33
10.8%
poulet5_1
36.3%
48%
101 bp
8%
0.3
poulet5_2
36.2%
48%
101 bp
8%
0.3
samtools_flagstat
20.7
samtools_stats
0.42%
0.0
0.6
100.0%
0.6
tophat_data
99.5%
0.3
+
+
+
+
+
+
+
General Statistics: Columns
+
+
+
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
+
+
+
+
+
+
+
+
Sort
+
Visible
+
Group
+
Column
+
Description
+
ID
+
Scale
+
+
+
+
+
+
||
+
+
+
+
featureCounts
+
% Assigned
+
% Assigned reads
+
percent_assigned
+
None
+
+
+
||
+
+
+
+
featureCounts
+
M Assigned
+
Assigned reads (millions)
+
Assigned
+
read_count
+
+
+
||
+
+
+
+
Picard
+
% Dups
+
MarkDuplicates - Percent Duplication
+
PERCENT_DUPLICATION
+
None
+
+
+
||
+
+
+
+
Picard
+
Insert Size
+
Median Insert Size, all read orientations (bp)
+
summed_median
+
None
+
+
+
||
+
+
+
+
Picard
+
Mean Insert Size
+
Mean Insert Size, all read orientations (bp)
+
summed_mean
+
None
+
+
+
||
+
+
+
+
Samtools Stats
+
Error rate
+
Error rate using CIGAR
+
error_rate
+
None
+
+
+
||
+
+
+
+
Samtools Stats
+
M Non-Primary
+
Non-primary alignments (millions)
+
non-primary_alignments
+
read_count
+
+
+
||
+
+
+
+
Samtools Stats
+
M Reads Mapped
+
Reads Mapped in the bam file (millions)
+
reads_mapped
+
read_count
+
+
+
||
+
+
+
+
Samtools Stats
+
% Mapped
+
% Mapped Reads
+
reads_mapped_percent
+
None
+
+
+
||
+
+
+
+
Samtools Stats
+
M Total seqs
+
Total sequences in the bam file (millions)
+
raw_total_sequences
+
read_count
+
+
+
||
+
+
+
+
Samtools Flagstat
+
M Reads Mapped
+
Reads Mapped in the bam file (millions)
+
mapped_passed
+
read_count
+
+
+
||
+
+
+
+
Bismark
+
M Aligned
+
Total Aligned Sequences (millions)
+
aligned_reads
+
read_count
+
+
+
||
+
+
+
+
Bismark
+
% Aligned
+
Percent Aligned Sequences
+
percent_aligned
+
None
+
+
+
||
+
+
+
+
Tophat
+
% Aligned
+
overall read mapping rate
+
overall_aligned_percent
+
None
+
+
+
||
+
+
+
+
Tophat
+
M Aligned
+
Aligned reads, not multimapped or discordant (millions)
+
aligned_not_multimapped_discordant
+
read_count
+
+
+
||
+
+
+
+
Cutadapt
+
% Trimmed
+
% Total Base Pairs trimmed
+
percent_trimmed
+
None
+
+
+
||
+
+
+
+
FastQC
+
% Dups
+
% Duplicate Reads
+
percent_duplicates
+
None
+
+
+
||
+
+
+
+
FastQC
+
% GC
+
Average % GC Content
+
percent_gc
+
None
+
+
+
||
+
+
+
+
FastQC
+
Length
+
Average Sequence Length (bp)
+
avg_sequence_length
+
None
+
+
+
||
+
+
+
+
FastQC
+
% Failed
+
Percentage of modules failed in FastQC report (includes those not plotted here)
+
percent_fails
+
None
+
+
+
||
+
+
+
+
FastQC
+
M Seqs
+
Total Sequences (millions)
+
total_sequences
+
read_count
+
+
+
+
+
+
+
+
+
+
+
+
+
+
featureCounts
+
Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.
+
+
+
+
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
+
Picard
+
Picard is a set of Java command line tools for manipulating high-throughput sequencing data.
+
+
+
+
+
Mark Duplicates
+
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
Insert Size
+
+
Plot shows the number of reads at a given insert size. Reads with different orientations are summed.
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
GC Coverage Bias
+
+
This plot shows bias in coverage across regions of the genome with varying GC content. A perfect library would be a flat line at y = 1.
loading..
+
+
+
+
+
+
+
+
+
+
Samtools
+
Samtools is a suite of programs for interacting with high-throughput sequencing data.
+
+
+
+
+
Percent Mapped
+
+
Alignment metrics from samtools stats; mapped vs. unmapped reads.
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
Alignment metrics
+
+
This module parses the output from samtools stats. All numbers in millions.
+
loading..
+
+
+
+
+
+
+
+
+
Samtools Flagstat
+
+
This module parses the output from samtools flagstat. All numbers in millions.
+
loading..
+
+
+
+
+
+
+
+
+
+
Bismark
+
Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.
+
+
+
+
+
Alignment Rates
+
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
Strand Alignment
+
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
+
Tophat
+
Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes.
+
+
+
+
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
+
Cutadapt
+
Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.
+
+
+
+
+
This plot shows the number of reads with certain lengths of adapter trimmed.
+ Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak
+ may be related to adapter length. See the
+ cutadapt documentation
+ for more information on how these numbers are generated.
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
+
FastQC
+
FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.
+
+
+
+
+
Sequence Quality Histograms
+
+
The mean quality value across each base position in the read. See the FastQC help.
loading..
+
+
+
+
+
+
+
+
+
Per Sequence Quality Scores
+
+
The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.
loading..
+
+
+
+
+
+
+
+
+
Per Base Sequence Content
+
+
The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.
+
+
+ Click a sample row to see a line plot for that dataset.
+
+
Rollover for sample name
+
+
+ Position: -
+
%T: -
+
%C: -
+
%A: -
+
%G: -
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Per Sequence GC Content
+
+
The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.
+ See the FastQC help.
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
Per Base N Content
+
+
The percentage of base calls at each position for which an N was called. See the FastQC help.
loading..
+
+
+
+
+
+
+
+
+
Sequence Length Distribution
+
+
All samples have sequences of a single length (101bp).
+
+
+
+
+
+
+
+
Sequence Duplication Levels
+
+
The relative level of duplication found for every sequence. See the FastQC help.
2 samples had less than 1% of reads made up of overrepresented sequences
+
+
+
+
+
+
+
+
Adapter Content
+
+
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.
No samples found with any adapter contamination > 0.1%
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Plot Table Data
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
+
+
+
+
+
+
+
+
Sort
+
Visible
+
Group
+
Column
+
Description
+
ID
+
Scale
+
+
+
+
+
+
||
+
+
+
+
Bismark
+
M Aligned
+
Total Aligned Sequences (millions)
+
aligned_reads
+
read_count
+
+
+
||
+
+
+
+
Bismark
+
% Aligned
+
Percent Aligned Sequences
+
percent_aligned
+
None
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Bismark
+
Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.
+
+
+
+
+
Alignment Rates
+
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
Strand Alignment
+
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Plot Table Data
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
+
+
+
+
+
+
+
+
Sort
+
Visible
+
Group
+
Column
+
Description
+
ID
+
Scale
+
+
+
+
+
+
||
+
+
+
+
Bowtie 2
+
% Aligned
+
overall alignment rate
+
overall_alignment_rate
+
None
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Bowtie 2
+
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
+
+
+
+
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Plot Table Data
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
+
+
+
+
+
+
+
+
Sort
+
Visible
+
Group
+
Column
+
Description
+
ID
+
Scale
+
+
+
+
+
+
||
+
+
+
+
Cutadapt
+
% Trimmed
+
% Total Base Pairs trimmed
+
percent_trimmed
+
None
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Cutadapt
+
Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.
+
+
+
+
+
This plot shows the number of reads with certain lengths of adapter trimmed.
+ Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak
+ may be related to adapter length. See the
+ cutadapt documentation
+ for more information on how these numbers are generated.
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Plot Table Data
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
1 samples had less than 1% of reads made up of overrepresented sequences
+
+
+
+
+
+
+
+
Adapter Content
+
+
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.
No samples found with any adapter contamination > 0.1%
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Plot Table Data
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
2 samples had less than 1% of reads made up of overrepresented sequences
+
+
+
+
+
+
+
+
Adapter Content
+
+
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.
No samples found with any adapter contamination > 0.1%
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Plot Table Data
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
70: TopHat on data 1, data 4, and data 3: accepted_hits
70.8%
0.3
75: TopHat on data 1, data 6, and data 5: accepted_hits
69.6%
0.4
80: TopHat on data 1, data 8, and data 7: accepted_hits
71.8%
0.4
85: TopHat on data 1, data 10, and data 9: accepted_hits
72.0%
0.4
90: TopHat on data 1, data 12, and data 11: accepted_hits
71.3%
0.4
95: TopHat on data 1, data 14, and data 13: accepted_hits
70.7%
0.5
+
+
+
+
+
+
+
General Statistics: Columns
+
+
+
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
+
+
+
+
+
+
+
+
Sort
+
Visible
+
Group
+
Column
+
Description
+
ID
+
Scale
+
+
+
+
+
+
||
+
+
+
+
featureCounts
+
% Assigned
+
% Assigned reads
+
percent_assigned
+
None
+
+
+
||
+
+
+
+
featureCounts
+
M Assigned
+
Assigned reads (millions)
+
Assigned
+
read_count
+
+
+
+
+
+
+
+
+
+
+
+
+
+
featureCounts
+
Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.
+
+
+
+
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Plot Table Data
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
+
+
+
+
+
+
+
+
Sort
+
Visible
+
Group
+
Column
+
Description
+
ID
+
Scale
+
+
+
+
+
+
||
+
+
+
+
HTSeq Count
+
% Assigned
+
% Assigned reads
+
percent_assigned
+
None
+
+
+
||
+
+
+
+
HTSeq Count
+
M Assigned
+
Assigned Reads (millions)
+
assigned
+
read_count
+
+
+
+
+
+
+
+
+
+
+
+
+
+
HTSeq Count
+
HTSeq Count is part of the HTSeq Python package - it takes a file with aligned sequencing reads, plus a list of genomic features and counts how many reads map to each feature.
+
+
+
+
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Plot Table Data
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
+
+
+
+
+
+
+
+
Sort
+
Visible
+
Group
+
Column
+
Description
+
ID
+
Scale
+
+
+
+
+
+
||
+
+
+
+
Picard
+
% rRNA
+
Percent of aligned bases overlapping ribosomal RNA regions
+
PCT_RIBOSOMAL_BASES
+
None
+
+
+
||
+
+
+
+
Picard
+
% mRNA
+
Percent of aligned bases overlapping UTRs and coding regions of mRNA transcripts
+
PCT_MRNA_BASES
+
None
+
+
+
||
+
+
+
+
Picard
+
% Dups
+
MarkDuplicates - Percent Duplication
+
PERCENT_DUPLICATION
+
None
+
+
+
||
+
+
+
+
Picard
+
Insert Size
+
Median Insert Size, all read orientations (bp)
+
summed_median
+
None
+
+
+
||
+
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+
+
Picard
+
Mean Insert Size
+
Mean Insert Size, all read orientations (bp)
+
summed_mean
+
None
+
+
+
||
+
+
+
+
Picard
+
% Aligned
+
Percent of aligned reads
+
PCT_PF_READS_ALIGNED
+
None
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Picard
+
Picard is a set of Java command line tools for manipulating high-throughput sequencing data.
+
+
+
+
+
Mark Duplicates
+
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
Insert Size
+
+
Plot shows the number of reads at a given insert size. Reads with different orientations are summed.
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
Base Distribution
+
+
Plot shows the distribution of bases by cycle.
+
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+
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+
+
loading..
+
+
+
+
+
+
+
+
+
GC Coverage Bias
+
+
This plot shows bias in coverage across regions of the genome with varying GC content. A perfect library would be a flat line at y = 1.
loading..
+
+
+
+
+
+
+
+
+
RnaSeqMetrics Assignment
+
+
Number of bases in primary alignments that align to regions in the reference genome.
+
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+
+
loading..
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+
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+
+
+
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+
+
Gene Coverage
+
+
loading..
+
+
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+
+
Alignment Summary
+
+
Plase note that Picard's read counts are divided by two for paired-end data.
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+
loading..
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+
Plot Table Data
+
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+
+
+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.
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loading..
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+
Plot Table Data
+
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+
+
+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
+
+
+
+
+
+
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+
Sort
+
Visible
+
Group
+
Column
+
Description
+
ID
+
Scale
+
+
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+
+
||
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+
Samtools Stats
+
Error rate
+
Error rate using CIGAR
+
error_rate
+
None
+
+
+
||
+
+
+
+
Samtools Stats
+
M Non-Primary
+
Non-primary alignments (millions)
+
non-primary_alignments
+
read_count
+
+
+
||
+
+
+
+
Samtools Stats
+
M Reads Mapped
+
Reads Mapped in the bam file (millions)
+
reads_mapped
+
read_count
+
+
+
||
+
+
+
+
Samtools Stats
+
% Mapped
+
% Mapped Reads
+
reads_mapped_percent
+
None
+
+
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||
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+
+
+
Samtools Stats
+
M Total seqs
+
Total sequences in the bam file (millions)
+
raw_total_sequences
+
read_count
+
+
+
||
+
+
+
+
Samtools Flagstat
+
M Reads Mapped
+
Reads Mapped in the bam file (millions)
+
mapped_passed
+
read_count
+
+
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+
+
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+
+
+
+
+
+
+
+
Samtools
+
Samtools is a suite of programs for interacting with high-throughput sequencing data.
+
+
+
+
+
Percent Mapped
+
+
Alignment metrics from samtools stats; mapped vs. unmapped reads.
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
Alignment metrics
+
+
This module parses the output from samtools stats. All numbers in millions.
+
loading..
+
+
+
+
+
+
+
+
+
Samtools Flagstat
+
+
This module parses the output from samtools flagstat. All numbers in millions.
+
loading..
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+
+
Plot Table Data
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
Samtools is a suite of programs for interacting with high-throughput sequencing data.
+
+
+
+
+
XY counts
+
+
+
+
+
+
loading..
+
+
+
+
+
+
+
+
+
Mapped reads per contig
+
+
The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.
+
+
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+
+
loading..
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+
Plot Table Data
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
+ MultiQC: Summarize analysis results for multiple tools and samples in a single report
+ Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
+ Bioinformatics (2016)
+ doi: 10.1093/bioinformatics/btw354
+ PMID: 27312411
+
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
+
+
+
+
+
+
+
+
Sort
+
Visible
+
Group
+
Column
+
Description
+
ID
+
Scale
+
+
+
+
+
+
||
+
+
+
+
Tophat
+
% Aligned
+
overall read mapping rate
+
overall_aligned_percent
+
None
+
+
+
||
+
+
+
+
Tophat
+
M Aligned
+
Aligned reads, not multimapped or discordant (millions)
+
aligned_not_multimapped_discordant
+
read_count
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Tophat
+
Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes.
+
+
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+
+
loading..
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+
Plot Table Data
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+
+
+
+
+
+
Regex Help
+
+
+
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
TopHat on data 1, data 14, and data 13: align_summary
99.5%
0.3
dataset_114.dat]
0.6%
dataset_197.dat
176
poulet5_1
36.3%
48%
101
0.3
poulet5_2
36.2%
48%
101
0.3
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General Statistics: Columns
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Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
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featureCounts
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% Assigned
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% Assigned reads
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featureCounts
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M Assigned
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Assigned reads (millions)
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read_count
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Picard
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% Dups
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MarkDuplicates - Percent Duplication
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Picard
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Insert Size
-
Median Insert Size, all read orientations (bp)
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Picard
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Fold Enrichment
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Fold Enrichment
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Picard
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Target Bases 30X
-
Percent of target bases with coverage ≥ 30X
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Picard
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CCG Oxidation
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CCG-CAG Oxidation Error Rate
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Samtools
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M Total seqs
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Total sequences in the bam file
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read_count
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Samtools
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M Reads Mapped
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Reads Mapped in the bam file
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read_count
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Samtools
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M Non-Primary Alignments
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Non primary alignment (millions)
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read_count
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Samtools
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Error rate
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Error rate using CIGAR
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Bismark
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% mCpG
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% Cytosines methylated in CpG context
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Bismark
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% mCHG
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% Cytosines methylated in CHG context
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Bismark
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% mCHH
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% Cytosines methylated in CHH context
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Bismark
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M C's
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Total number of C's analysed, in millions
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Bismark
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% Dups
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Percent Duplicated Alignments
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Bismark
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M Unique
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Deduplicated Alignments (millions)
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read_count
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Bismark
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M Aligned
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Total Aligned Sequences (millions)
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read_count
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Bismark
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% Aligned
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Percent Aligned Sequences
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Tophat
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% Aligned
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overall read mapping rate
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Tophat
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M Aligned
-
Aligned reads, not multimapped or discordant (millions)
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read_count
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Cutadapt
-
% Trimmed
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% Total Base Pairs trimmed
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FastQC
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% Dups
-
% Duplicate Reads
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FastQC
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% GC
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Average % GC Content
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FastQC
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Length
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Average Sequence Length (bp)
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FastQC
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M Seqs
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Total Sequences (millions)
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read_count
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featureCounts
-
Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.
-
-
-
loading..
-
-
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-
-
-
Picard
-
Picard is a set of Java command line tools for manipulating high-throughput sequencing data.
-
-
-
Mark Duplicates
-
-
-
-
loading..
-
-
-
-
-
-
-
Insert Size
-
Plot shows the number of reads at a given insert size. Reads with different orientations are summed.
-
-
-
-
-
loading..
-
-
-
-
-
-
GC Coverage Bias
-
This plot shows bias in coverage across regions of the genome with varying GC content. A perfect library would be a flat line at y = 1.
loading..
-
-
-
-
-
-
-
-
-
Samtools
-
Samtools is a suite of programs for interacting with high-throughput sequencing data. This module parses the output from samtools stats.
-
-
-
Reads Mapping
-
loading..
-
-
-
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Bases Mapping
-
loading..
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Read Pairs
-
loading..
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Bismark
-
Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.
-
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-
Alignment Rates
-
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loading..
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Strand Alignment
-
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loading..
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Tophat
-
Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes.
-
-
-
loading..
-
-
-
-
-
-
-
-
Cutadapt
-
Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.
This plot shows the number of reads with certain lengths of adapter trimmed.
- Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak
- may be related to adapter length. See the
- cutadapt documentation
- for more information on how these numbers are generated.
-
-
-
-
-
loading..
-
-
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-
-
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FastQC
-
FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.
-
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Sequence Quality Histograms
-
The mean quality value across each base position in the read. See the FastQC help.
loading..
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Per Sequence Quality Scores
-
The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.
loading..
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Per Base Sequence Content
-
The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.
Click a heatmap row to see a line plot for that dataset.
-
rollover for sample name
-
- Position: -
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%T: -
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%C: -
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%A: -
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%G: -
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Per Sequence GC Content
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The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.
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loading..
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Per Base N Content
-
The percentage of base calls at each position for which an N was called. See the FastQC help.
loading..
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-
-
Sequence Length Distribution
-
All samples have sequences of exactly 101 bp in length.
-
-
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Sequence Duplication Levels
-
The relative level of duplication found for every sequence. See the FastQC help.
loading..
-
-
-
-
-
-
Adapter Content
-
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.
No samples found with any adapter contamination > 0.1%
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Regex Help
-
-
-
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
-
-
-
-
Sort
-
Visible
-
Group
-
Column
-
Description
-
Scale
-
-
-
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-
||
-
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Bismark
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M Aligned
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Total Aligned Sequences (millions)
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read_count
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Bismark
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% Aligned
-
Percent Aligned Sequences
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Bismark
-
Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.
-
-
-
Alignment Rates
-
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-
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loading..
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Strand Alignment
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loading..
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-
-
-
-
Regex Help
-
-
-
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
-
-
-
-
Sort
-
Visible
-
Group
-
Column
-
Description
-
Scale
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Cutadapt
-
Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.
This plot shows the number of reads with certain lengths of adapter trimmed.
- Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak
- may be related to adapter length. See the
- cutadapt documentation
- for more information on how these numbers are generated.
-
-
-
-
-
loading..
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Regex Help
-
-
-
Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
-
-
-
-
Sort
-
Visible
-
Group
-
Column
-
Description
-
Scale
-
-
-
-
-
-
||
-
-
-
-
FastQC
-
% Dups
-
% Duplicate Reads
-
-
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||
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FastQC
-
% GC
-
Average % GC Content
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||
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FastQC
-
Length
-
Average Sequence Length (bp)
-
-
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||
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FastQC
-
M Seqs
-
Total Sequences (millions)
-
read_count
-
-
-
-
-
-
-
-
-
-
-
-
-
-
FastQC
-
FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.
-
-
-
Sequence Quality Histograms
-
The mean quality value across each base position in the read. See the FastQC help.
loading..
-
-
-
-
-
-
Per Sequence Quality Scores
-
The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.
loading..
-
-
-
-
-
-
Per Base Sequence Content
-
The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.
Click a heatmap row to see a line plot for that dataset.
-
rollover for sample name
-
- Position: -
-
%T: -
-
%C: -
-
%A: -
-
%G: -
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Per Sequence GC Content
-
The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.
-
-
-
-
-
loading..
-
-
-
-
-
-
Per Base N Content
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The percentage of base calls at each position for which an N was called. See the FastQC help.
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Sequence Length Distribution
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All samples have sequences of exactly 101 bp in length.
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Sequence Duplication Levels
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The relative level of duplication found for every sequence. See the FastQC help.
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Adapter Content
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The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.
No samples found with any adapter contamination > 0.1%
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Regex Help
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Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
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FastQC
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% Dups
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% Duplicate Reads
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FastQC
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% GC
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Average % GC Content
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FastQC
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Length
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Average Sequence Length (bp)
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FastQC
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M Seqs
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Total Sequences (millions)
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read_count
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FastQC
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FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.
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Sequence Quality Histograms
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The mean quality value across each base position in the read. See the FastQC help.
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Per Sequence Quality Scores
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The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.
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Per Base Sequence Content
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The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.
Click a heatmap row to see a line plot for that dataset.
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Per Sequence GC Content
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The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.
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Per Base N Content
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The percentage of base calls at each position for which an N was called. See the FastQC help.
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Sequence Length Distribution
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All samples have sequences of exactly 101 bp in length.
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Sequence Duplication Levels
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The relative level of duplication found for every sequence. See the FastQC help.
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Adapter Content
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The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.
No samples found with any adapter contamination > 0.1%
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Regex Help
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Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
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featureCounts
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% Assigned
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% Assigned reads
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featureCounts
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Assigned reads (millions)
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read_count
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featureCounts
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Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.
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Regex Help
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Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.
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Picard
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% Dups
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MarkDuplicates - Percent Duplication
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Picard
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Insert Size
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Median Insert Size, all read orientations (bp)
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Fold Enrichment
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Fold Enrichment
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Picard
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Target Bases 30X
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Percent of target bases with coverage ≥ 30X
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Picard
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CCG Oxidation
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CCG-CAG Oxidation Error Rate
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Picard
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Picard is a set of Java command line tools for manipulating high-throughput sequencing data.
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Mark Duplicates
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Insert Size
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Plot shows the number of reads at a given insert size. Reads with different orientations are summed.
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GC Coverage Bias
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This plot shows bias in coverage across regions of the genome with varying GC content. A perfect library would be a flat line at y = 1.
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Regex Help
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Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
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Samtools
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Total sequences in the bam file
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read_count
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Samtools
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Reads Mapped in the bam file
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Samtools
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Non primary alignment (millions)
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Samtools
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Error rate
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Error rate using CIGAR
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Samtools
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Samtools is a suite of programs for interacting with high-throughput sequencing data. This module parses the output from samtools stats.
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Reads Mapping
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Bases Mapping
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Read Pairs
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Regex Help
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Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
TopHat on data 1, data 14, and data 13: align_summary
99.5%
0.3
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General Statistics: Columns
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overall read mapping rate
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Aligned reads, not multimapped or discordant (millions)
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Tophat
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Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes.
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Regex Help
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Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.
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