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* This is doMreps verion 0.2 *
* *
* 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 <list of fastq files>
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.