Dinh:RRBS MONOD Analysis/Mapping
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RRBS data mapping
Trim with trim-galore
- use longer adapter sequences to trim more of adaptor sequences
- Trim-galore command:
/home/ddiep/softwares/trim_galore_latest/trim_galore --phred64 --rrbs --paired --dont_gzip -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
Stitch PE reads with COPE
- use simple mode
- COPE command:
/home/ddiep/softwares/cope-src-v1.1.3/src/cope -o connect.fq -2 left1.fq -3 left2.fq -m 0
- After cope, merge all of the files to one:
cat connect.fq left1.fq left2.fq > $n.fq
Process reads with Bisreadmapper
- Use hg19_lambda references
- Use bwa-mem for mapping
- Do not remove duplicates
- Do not generate pileup and bed files
- BisReadMapper command:
$scripts_dir/BisReadMapper.pl -r $reads_dir/${n}.fq -W $template_fwd -C $template_rev -g $ref_fai -a $bwa -b 64 -p 4 -n $n > $n.status
- BamExtractor command:
$scripts_dir/BamExtractor.pl -i list_sams -s $cur_dir/list_paths_Hg19 -o $n -r none -v no -b no -p no -d 5
Merge sorted BAM files with master script
- Master merge script: File:RRBS MONOD mergeBamFiles.txt