/doMreps-Mac-OS-X-Darwin

doMreps for Mac OS X / Darwin

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doMreps-Mac-OS-X-Darwin

doMreps for Mac OS X / Darwin

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*             This is doMreps verion 0.2 compiled             *
*                    for Mac OS X / Darwin                    *
*                                                             *
* released under GNU General Public Licence (see LICENCE.md)  *
*                                                             *
*                                                             *
*      This program is a wrapper to the mreps program         *
*                (http://mreps.univ-mlv.fr/)                  *
*                                                             *
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  • This program is free software: you can redistribute it and/or modify

  • it under the terms of the GNU General Public License as published by

  • the Free Software Foundation, either version 3 of the License, or

  • (at your option) any later version.

  • This program is distributed in the hope that it will be useful,

  • but WITHOUT ANY WARRANTY; without even the implied warranty of

  • MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

  • GNU General Public License for more details.

  • You should have received a copy of the GNU General Public License

  • along with this program. If not, see http://www.gnu.org/licenses/.

  • WARNING: doMreps use a slightly modified version of mreps.

  • The original version should be downloaded from

  • http://mreps.univ-mlv.fr/.

  • The aim of the modification was to have a less verbose output to

  • accelerate the processing (a more specific output for fastq data)

  • mreps is released by the author under the GNU GPL licence

  • (see LICENCE.md)

  • This programm runs under linux 64 bits

  • and requires perl to be installed

Usage: perl doMreps.pl count occurrences of internal tandem duplication

Examples: perl doMreps sample1/*.fastq

doMreps$ ./doMreps-0.2.pl sample1/*.fastq opening file sample1/sample1_S4._L001_peared_001.fastq ADD : 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

ITD SEED ITD SEED WT+ITD MREPS sample1/sample1_S4._L001_peared_001.fastq ITD sample1/sample1_S4._L001_peared_001.fastq WT+ITD #reads 517974 517974 AGATAATGAGTACTTCTACGTTGA TTCTACGTTGAAGATAATGAG ATAATGAGTACTTCTACGTTGA 6899 0 185181 AGCCAATGAGTACTTCTACGTTGA TTCTACGTTGAAGCCAATGAG CCAATGAGTACTTCTACGTTGA 6245 41379 39335 CCCCTCCCATCCCTGAGGCTTCCCCAGCAGGTGGGACACAGCACACAGGC AGCACACAGGCCCCCTCCCAT AGGTGGGACACAGCACACAGGC 114 1021 2723 CACAGCACACAGGACCCCTCCCATCCCTGAGGCTTTCCCAGCAGGTGGGA AGCAGGTGGGACACAGCACAC GAGGCTTTCCCAGCAGGTGGGA 61 2832 1238 AAGCCTGTGTGCTGTGTCCCACCTGCTGGGGAAGCCTCAGGGATGGGAGGGG GATGGGAGGGGAAGCCTGTGT GAAGCCTCAGGGATGGGAGGGG 35 414 1310 GGGGAAGCCTGTGTGCTGTGTCCCACCTGCTGGGGAAGCCTCGGGGATGGGA CGGGGATGGGAGGGGAAGCCT TGGGGAAGCCTCGGGGATGGGA 28 384 451

Output description: Each time mreps find a new Internal Tandem Duplication (ITD), it displays an 'F' (for Forward read) or an 'R' (for Reverse read). Then it displays a tabular view of ITDs. First line is the column header. Second line is the total number of reads. Then we have for each ITD sequence, the seed used for counting ITD reads, the seed used for counting WT and ITD reads, the number of ITD found by mreps for all samples then for each fastq file: the number of reads with the ITD seed, the number of reads with the WT or ITD seed.