Dinh:COMPUTATIONAL/bisReadMapper: Difference between revisions

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=MOST CURRENT scripts: refer to the following wiki pages instead!!!=
=MOST CURRENT scripts: refer to the following wiki pages=
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2013/NOTES/2013-1-7] January 7, 2013.
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2013/NOTES/2013-1-7] January 7, 2013.
==To perform bisulfite reads mapping with bisReadMapper==
===Know where the following files and software are:===
# Reference index
# soap or bowtie2: currently I have bowtie2 running with --fast setting, which seems to be a lot slower than soap. this setting may be changed to --very-fast in the future for mapping BSPP data.
#samtools
#reads (do not need to copy the reads to the current directory, nor concatenate them)
#Methylation pipeline scripts (make sure you are either using the Triton version or the single-server version). The Triton version will make a number of job submissions!
===Master shell script: 1 - perform mapping.===
*This master script process bisulfite reads.
*Change this to use the correct reference genome. Either bisHg19 or bisMm9.
*Change /home/ddiep/scripts to the correct path of the MethylationPipeline.
<nowiki>
My_ref="/projects/zhang-lab/ddiep/bisHg19"
bisReadMapper="/home/ddiep/scripts/MethylationPipeline/bisReadMapper_Bowtie2.pl"
for f in list_*
do
        g=`echo $f | sed 's/list_//g'`
        /home/ddiep/scripts/MethylationPipeline/wBOWTIE/submitBSPPMapJobs.pl $g $My_ref $bisReadMapper < $f
done </nowiki>
*To run this master script, we need to be in the working directory and we need to create "list_SAMPLENAME" files. Each list file is simply a list of the location and names of all the reads files:
    For single end:
    '''/projects/zhang-lab/ddiep/TEST/s_6_1_Indx10.txt'''
    '''/projects/zhang-lab/ddiep/TEST/s_6_2_Indx10.txt'''
    For paired end:
    '''/projects/zhang-lab/ddiep/TEST/s_6_1_Indx10.txt /projects/zhang-lab/ddiep/TEST/s_6_2_Indx10.txt'''
*Command to run:
sh Go.mapBisulfiteReads.sh
===Master shell script: 2 - pull out methylation sites!===
*This master script process the mapped reads and call SNPs.
*Again, make the necessary modifications so that it is specific to your genome: change reference path and change the list of chromosomes so that they are correct.
*Again, make sure that the path to MethylationPipeline is correct.
<nowiki>
My_ref="/home/ddiep/bisHg19"
for f in list_*
do
        g=`echo $f | sed 's/list_//g'`
        # human
        for c in chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY chrM
        do
                /home/ddiep/scripts/MethylationPipeline/submitMergeAndExtractJobs.pl $g $c $My_ref 1
        done
done </nowiki>
*Command to run:
sh Go.mergeAndExtract.sh

Revision as of 02:58, 11 January 2013

MOST CURRENT scripts: refer to the following wiki pages

[1] January 7, 2013.