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annotate 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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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 .TH srf2fastq 1 "December 10" "" "Staden io_lib" |
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2 |
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3 .SH "NAME" |
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4 |
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5 .PP |
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6 .BR srf2fastq |
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7 \- Converts SRF files to Sanger fastq format |
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8 |
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9 .SH "SYNOPSIS" |
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10 .PP |
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11 \fBsrf2fastq\fR [\fIoptions\fR] \fIsrf_archive\fR ... |
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12 |
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13 .SH "DESCRIPTION" |
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14 .PP |
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15 \fBsrf2fastq\fR extracts sequences and qualities from one or more SRF |
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16 archives and writes them in Sanger fastq format to stdout. |
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17 .PP |
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18 Note that Illumina |
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19 also have a fastq format (used in the GERALD directories) which |
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20 differs slightly in the use of log-odds scores for the quality |
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21 values. The format described here is using the traditional \fIPhred\fR |
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22 style of quality encoding. |
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23 |
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24 .SH "OPTIONS" |
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25 .PP |
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26 .TP |
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27 \fB-c\fR |
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28 Outputs calibrated confidence values using the ZTR \fBCNF1\fR |
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29 chunk type for a single quality per base. Without this use the |
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30 original Illumina \fI_prb.txt\fR files consisting of four quality |
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31 values per base, stored in the ZTR \fBCNF4\fR chunks. |
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32 .TP |
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33 \fB-C\fR |
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34 Masks out sequences tagged as bad quality. |
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35 .TP |
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36 \fB-s\fR \fIroot\fR |
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37 Generates files on disk with filenames starting \fIroot\fR, one file |
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38 per non-explicit element in the SRF/ZTR region (REGN) chunk. Typically |
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39 this results in two files for paired end runs. The filename suffixes |
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40 come from the names listed in the SRF region chunks. This |
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41 option conflicts with the \fB-S\fR parameter. |
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42 .TP |
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43 \fB-S\fR |
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44 Splits sequences into regions, but sequentially lists each sequence |
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45 region to stdout instead of splitting to separate files on disk. This |
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46 option conflicts with the \fB-s\fR parameter. |
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47 .TP |
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48 \fB-n\FR |
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49 When using -s the filename suffixes are simply numbered (starting with |
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50 1) instead of using the names listed in the SRF region chunks. |
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51 .TP |
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52 \fB-a\fR |
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53 Appends region index to the sequence names. Ie generate "name/1" and |
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54 "name/2" for a paired read. |
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55 .TP |
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56 \fB-e\fR |
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57 Include any explicit sequence (ZTR region chunk of type 'E') in the |
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58 sequence output. The explicit sequence is also included in the quality |
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59 line too. Currently this is utilised by ABI SOLiD to store the last |
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60 base of the primer. |
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61 .TP |
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62 \fB-r\fR \fIregion list\fR |
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63 Reverse complements the sequence and reverses the quality values for |
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64 all regions in the \fIregion list\fR. This is a comma separated list |
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65 of integer values enumerating the regions, starting from 1. Note that |
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66 this option only works when either \fB-s\fR or \fB-S\fR are |
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67 specified. |
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68 |
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69 .SH "EXAMPLES" |
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70 .PP |
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71 To extract only the good quality sequences from all srf files in the |
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72 current directory using calibrated confidence values (if available). |
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73 .PP |
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74 .nf |
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75 srf2fastq -c -C *.srf > runX.fastq |
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76 .fi |
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77 .PP |
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78 To extract a paired end run into two separate files with sequences |
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79 named \fIname\fR/1 and \fIname\fR/2. |
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80 .PP |
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81 .nf |
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82 srf2fastq -s runX -a -n runX.srf |
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83 .fi |
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84 .PP |
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85 To extract a paired end run as a single file, alternating forward and |
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86 reverse sequences, with the second read being reverse complemented. |
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87 .PP |
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88 .nf |
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89 srf2fastq -S -r 2 runX.srf > runX.fastq |
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90 .fi |
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91 .SH "AUTHOR" |
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92 .PP |
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93 James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute |