Dinh:COMPUTATIONAL/bisReadMapper
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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.
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
- 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.
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 # mouse #for c in chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX chrY chrM do /home/ddiep/scripts/MethylationPipeline/submitMergeAndExtractJobs.pl $g $c $My_ref 1 done done
- Command to run:
sh Go.mergeAndExtract.sh