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comparison tools/fastq/fastq_paired_unpaired.xml @ 1:7ed81e36fc1c

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Uploaded v0.0.5 which handles Illumina 1.8 style pair naming.
author peterjc
date Mon, 12 Dec 2011 11:33:10 -0500
parents 72e9fcaec61f
children 95a632a71951
comparison
equal deleted inserted replaced
0:72e9fcaec61f 1:7ed81e36fc1c
1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.4"> 1 <tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.5">
2 <description>using the read name suffices</description> 2 <description>using the read name suffices</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 fastq_paired_unpaired.py $input_fastq.extension $input_fastq 4 fastq_paired_unpaired.py $input_fastq.extension $input_fastq
5 #if $output_choice_cond.output_choice=="separate" 5 #if $output_choice_cond.output_choice=="separate"
6 $output_forward $output_reverse 6 $output_forward $output_reverse
50 preserve this sort order. Pairing are recognised based on standard name 50 preserve this sort order. Pairing are recognised based on standard name
51 suffices. See below or run the tool with no arguments for more details. 51 suffices. See below or run the tool with no arguments for more details.
52 52
53 Any reads where the forward/reverse naming suffix used is not recognised 53 Any reads where the forward/reverse naming suffix used is not recognised
54 are treated as orphan reads. The tool supports the /1 and /2 convention 54 are treated as orphan reads. The tool supports the /1 and /2 convention
55 used by Illumina, the .f and .r convention, and the Sanger convention 55 originally used by Illumina, .f and .r convention, the Sanger convention
56 (see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details). 56 (see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details),
57 and the current Illumina convention where the reads get the same identifier
58 with the fragment number in the description, for example:
59
60 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA
61 * @HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 2:N:0:TGNCCA
57 62
58 Note that this does support multiple forward and reverse reads per template 63 Note that this does support multiple forward and reverse reads per template
59 (which is quite common with Sanger sequencing), e.g. this which is sorted 64 (which is quite common with Sanger sequencing), e.g. this which is sorted
60 alphabetically: 65 alphabetically:
61 66
62 WTSI_1055_4p17.p1kapIBF 67 * WTSI_1055_4p17.p1kapIBF
63 WTSI_1055_4p17.p1kpIBF 68 * WTSI_1055_4p17.p1kpIBF
64 WTSI_1055_4p17.q1kapIBR 69 * WTSI_1055_4p17.q1kapIBR
65 WTSI_1055_4p17.q1kpIBR 70 * WTSI_1055_4p17.q1kpIBR
66 71
67 or this where the reads already come in pairs: 72 or this where the reads already come in pairs:
68 73
69 WTSI_1055_4p17.p1kapIBF 74 * WTSI_1055_4p17.p1kapIBF
70 WTSI_1055_4p17.q1kapIBR 75 * WTSI_1055_4p17.q1kapIBR
71 WTSI_1055_4p17.p1kpIBF 76 * WTSI_1055_4p17.p1kpIBF
72 WTSI_1055_4p17.q1kpIBR 77 * WTSI_1055_4p17.q1kpIBR
73 78
74 both become: 79 both become:
75 80
76 WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR 81 * WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR
77 WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR 82 * WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR
78 83
79 </help> 84 </help>
80 </tool> 85 </tool>