# HG changeset patch # User devteam # Date 1380121341 14400 # Node ID b145b9b2664861961728f2141d24744d5054a150 Uploaded tool tarball. diff -r 000000000000 -r b145b9b26648 fastq_quality_filter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_quality_filter.xml Wed Sep 25 11:02:21 2013 -0400 @@ -0,0 +1,83 @@ + + + + fastx_toolkit + + zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output +#if $input.ext == "fastqsanger": +-Q 33 +#end if + + + + + + + Quality cut-off value + + + + Percent of bases in sequence that must have quality equal to / higher than cut-off value + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool filters reads based on quality scores. + +.. class:: infomark + +Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value. + +.. class:: infomark + +Using **percent = 50** requires the median quality of the cycles (in each read) to be at least the quality cut-off value. + +-------- + +Quality score distribution (of all cycles) is calculated for each read. If it is lower than the quality cut-off value - the read is discarded. + + +**Example**:: + + @CSHL_4_FC042AGOOII:1:2:214:584 + GACAATAAAC + +CSHL_4_FC042AGOOII:1:2:214:584 + 30 30 30 30 30 30 30 30 20 10 + +Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30). + +Using **percent = 90** and **cut-off = 30** - This read will be discarded (90% of the cycles do no have quality equal to / higher than 30). + +Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20). + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + diff -r 000000000000 -r b145b9b26648 test-data/fastq_qual_filter1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_qual_filter1.fastq Wed Sep 25 11:02:21 2013 -0400 @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +aaaaaaaaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE diff -r 000000000000 -r b145b9b26648 test-data/fastq_qual_filter1a.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_qual_filter1a.out Wed Sep 25 11:02:21 2013 -0400 @@ -0,0 +1,4 @@ +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa diff -r 000000000000 -r b145b9b26648 test-data/fastq_qual_filter1b.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_qual_filter1b.out Wed Sep 25 11:02:21 2013 -0400 @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa diff -r 000000000000 -r b145b9b26648 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 25 11:02:21 2013 -0400 @@ -0,0 +1,6 @@ + + + + + +