Mercurial > repos > dawe > srf2fastq
comparison srf2fastq/io_lib-1.12.2/man/man1/srf2fastq.1~ @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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1 .TH srf2fastq 1 "December 10" "" "Staden io_lib" | |
2 | |
3 .SH "NAME" | |
4 | |
5 .PP | |
6 .BR srf2fastq | |
7 \- Converts SRF files to Sanger fastq format | |
8 | |
9 .SH "SYNOPSIS" | |
10 .PP | |
11 \fBsrf2fastq\fR [\fIoptions\fR] \fIsrf_archive\fR ... | |
12 | |
13 .SH "DESCRIPTION" | |
14 .PP | |
15 \fBsrf2fastq\fR extracts sequences and qualities from one or more SRF | |
16 archives and writes them in Sanger fastq format to stdout. | |
17 .PP | |
18 Note that Illumina | |
19 also have a fastq format (used in the GERALD directories) which | |
20 differs slightly in the use of log-odds scores for the quality | |
21 values. The format described here is using the traditional \fIPhred\fR | |
22 style of quality encoding. | |
23 | |
24 .SH "OPTIONS" | |
25 .PP | |
26 .TP | |
27 \fB-c\fR | |
28 Outputs calibrated confidence values using the ZTR \fBCNF1\fR | |
29 chunk type for a single quality per base. Without this use the | |
30 original Illumina \fI_prb.txt\fR files consisting of four quality | |
31 values per base, stored in the ZTR \fBCNF4\fR chunks. | |
32 .TP | |
33 \fB-C\fR | |
34 Masks out sequences tagged as bad quality. | |
35 .TP | |
36 \fB-s\fR \fIroot\fR | |
37 Generates files on disk with filenames starting \fIroot\fR, one file | |
38 per non-explicit element in the SRF/ZTR region (REGN) chunk. Typically | |
39 this results in two files for paired end runs. The filename suffixes | |
40 come from the names listed in the SRF region chunks. | |
41 .TP | |
42 \fB-n\FR | |
43 When using -s the filename suffixes are simply numbered (starting with | |
44 1) instead of using the names listed in the SRF region chunks. | |
45 .TP | |
46 \fB-a\fR | |
47 Appends region index to the sequence names. Ie generate "name/1" and | |
48 "name/2" for a paired read. | |
49 .TP | |
50 \fB-e\fR | |
51 Include any explicit sequence (ZTR region chunk of type 'E') in the | |
52 sequence output. The explicit sequence is also included in the quality | |
53 line too. Currently this is utilised by ABI SOLiD to store the last | |
54 base of the primer. | |
55 | |
56 .SH "EXAMPLES" | |
57 .PP | |
58 To extract only the good quality sequences from all srf files in the | |
59 current directory using calibrated confidence values (if available). | |
60 .PP | |
61 .nf | |
62 srf2fastq -c -C *.srf > runX.fastq | |
63 .fi | |
64 .PP | |
65 To extract a paired end run into two separate files with sequences | |
66 named \fIname\fR/1 and \fIname\fR/2. | |
67 .PP | |
68 .nf | |
69 srf2fastq -s runX -a -n runX.srf | |
70 .fi | |
71 .SH "AUTHOR" | |
72 .PP | |
73 James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute |