https://github.com/nylander/454_tag_sorting

Script for finding paired tags ("Binladen tags") in 454 data
https://github.com/nylander/454_tag_sorting

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Script for finding paired tags ("Binladen tags") in 454 data

• Host: GitHub
• URL: https://github.com/nylander/454_tag_sorting
• Owner: nylander
• Created: 2014-01-22T14:54:34.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2014-01-22T15:07:25.000Z (over 12 years ago)
• Last Synced: 2023-03-24T03:25:11.632Z (about 3 years ago)
• Language: Perl
• Size: 137 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
454_tag_sorting

===============

Script for finding paired tags ("Binladen tags") in 454 data

NOTE: Work in progress!

-----------------------

Split files based on information on "paired tags". Sequencing approach described in

    Binladen et al. 2007. The Binladen J, Gilbert MTP, Bollback JP, Panitz F, Bendixen C, et al. (2007) The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing. PLoS ONE 2(2): e197. doi:10.1371/journal.pone.0000197

Documentation for find_tag_pairs.pl

-----------------------------------

                   FILE:  find_tag_pairs.pl

                  USAGE:  See ./find_tag_pairs.pl --help

                          ./find_tag_pairs.pl  -t=tags.tab  dat.fas

                          ./find_tag_pairs.pl  -t=tags.tab  -o=out.fas  dat.fas

                          ./find_tag_pairs.pl  -t=tags.tab  -r=rejects.fas  -o=out.fas  dat.fas

                          ./find_tag_pairs.pl  -t=tags.tab  --mask  -o=out.fas  dat.fas

                          ./find_tag_pairs.pl  -t=tags.tab  -o=out.fas --norejectfile --nosplit --nomask  dat.fas

                          ./find_tag_pairs.pl  -t=tags.tab  dat.fas  >  dat.retag.fas

                          ./find_tag_pairs.pl  -t=tags.tab  dat.fas.gz  |  gzip  >  dat.retag.fas.gz

                          ./find_tag_pairs.pl  -t=tags.tab  dat.fas.gz  |  zip  >  dat.retag.fas.zip

                OPTIONS:  -t=, --tagfile=    Specify  with tags.

                          -o=, --outfile=    Specify outfile (optional).

                          -r=, --rejectfile= Specify reject file (optional).

                          -nor, --norejectfile           Do not print reject file.

                          -m, --mask                     Mask (lower case) the matched parts of the sequence.

                          -nom, --nomask                 Do not mask. Default.

                          -s, --split                    Split found sequences into tag-specific files. Default.

                          -nos, --nosplit                Do not print separate files.

                          -h, --help                     Prints usage.

                          -v, --verbose                  Be verbose.

                          --noverbose                    Be quiet.

            DESCRIPTION:  Reads fasta file, primarily from a 454 sequencing run where samples have "paired tags" (see below), and

                          searches the sequences for tag pairs (specified in the tag-file, see below) in the end of the sequences.

                          If both tags in the pair is found, the sequence is captured, labelled and printed to STDOUT and/or to file.

                          Note: the match needs to be exact, i.e., all sequences with any mismatches will be rejected and put in

                          the rejects file.

                          Input SEQUENCE FILE:

                          Expected input sequence (Update 09/03/2013 10:03:50 AM: The lengths of the sequences are taken from the tags.tab file):

                           MID-tag 1 (11 bp)  Tag 1 (6 bp)  Forward primer (25 bp)  The Sequence  Reverse primer (20 bp) Tag 2 (6 bp)  MID-tag 2 (11 bp)

                          |-----------------|-------------|-----------------------|--------------|----------------------|------------|-----------------|

                          Sequence length of all tags and primers: 11+6+25+X+20+6+11 = 79+X

                          The string ' mytag=' will also be added to the fasta header. For example:

                           >H4XH63U01BXA6A rank=0176223 x=672.0 y=1344.0 length=383 mytag=MID4_L4_M6

                          Note: in this example, the length in the original label 'length=' will not be changed when trimming the output sequence.

                          Input TAGFILE:

                          The file with tags needs to be formatted this way (tab- or white-space separated columns). The header

                          ("Name_primer_tag" etc) is optional, but if present, should look like this. Pay close attention to

                          how the sequences are arranged and concatenated.

                          Name_primer_tag Name_primer_tag_mid Fwd_mid Fwd_tag Rev_mid Rev_tag Fwd_mid_Fwd_tag Rev_tag_Rev_mid

                          LCO_1_MLepR1_1 MID1_L1_M1 ACACGACGACT TACAAG AGTCGTGGTGT CTTGTA ACACGACGACTTACAAG CTTGTAAGTCGTGGTGT

                          LCO_1_MLepR1_2 MID1_L1_M2 ACACGACGACT TACAAG AGTCGTGGTGT GGTGTA ACACGACGACTTACAAG GGTGTAAGTCGTGGTGT

           REQUIREMENTS:  ---

                   BUGS:  Prints zero length sequences in STDOUT stream (IE4ERIL01ATX89, IE4ERIL01BF6K8, IE4ERIL01C0YQU, IE4ERIL01CAV50, IE4ERIL01CSZOX, IE4ERIL01DNOAW)

                  NOTES:  ---

                 AUTHOR:  Johan A. A. Nylander (JN), 

                COMPANY:  BILS

                VERSION:  1.0

                CREATED:  03/04/2011 07:45:16 PM CET

               REVISION:  09/03/2013 04:10:20 PM

                   TODO:  Solve zero-length sequence bug in output.