>Programmes > Teams > Gronemeyer Group



A miscellaneous of our favorite scripts used for massive parallel sequencing data processing... but not only.
SCRIPT   DESCRIPTION
bed2gff.pl   This script generates a simple GFF file (refer to http://www.sanger.ac.uk/Software/formats/GFF) from a BED file
bed2dummit2bed.pl   This script generates a simple bed file from bed file calculating the summit and adding N bps up- and down-stream. #    NOTE: the script consider as summit, the middle of the position given in the BED file. Be careful, sometimes BED position are made with merge peaks, so they could contain several summits.
BGIsoap2BED.pl   This script extracts Chr, Start and Strand from the soap aligned file and build a BED file
Bowtie2BED.pl   This script extracts Chr, Start and Strand from the default bowtie output aligment file and build a BED file
ChompFastqc.pl   This script chomps the tag sequenced in a fastaqc file to a determined length from 5' to 3'
CleanNonChrs.pl   This script removes the "extrange" chrs that may be you don't want to use (ex. random_chrs or chrM). CleanNonChrs can be used in MACS peak files as well.
CountMACSpeaks_pvalue.pl   This script generates an statistic counting the number of significant regions for different ranges of pvalue using a MACS peak file as input.
FilterFromTo.pl   This script filters peaks from the position X to the position Y from a ranking peaks list
##Model: MACS BED file
chr1 842378 842712 MACS_peak_1 137.33
chr1 939135 939618 MACS_peak_2 135.32
chr1 994325 995434 MACS_peak_3 884.34
FilterMACS_byParameter.pl   This script takes a MACS peak file and filters the sites using a selected parameter (by pvalue, by length, by FDR.. etc)
FilterTop.pl   This script filters the top N peaks from a bed file
##Model: MACS BED file
chr1 842378 842712 MACS_peak_1 137.33
chr1 939135 939618 MACS_peak_2 135.32
chr1 994325 995434 MACS_peak_3 884.34
SampleRandomLineFile.pl   This script selects N random lines from a file
SampleRandomLineFile_times.pl   This script selects N random lines from a file, by X times
     


Contact :
Marco Mendoza
Department of Cell Biology
IGBMC - B.P. 10142
F-67404 ILLKIRCH Cedex France
Tel: +33 (0) 3 88 65 34 19
marco.mendoza@igbmc.fr