Dinh:RRBS MONOD Analysis/Mapping

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RRBS data mapping[edit]

Trim with trim-galore[edit]

  • use longer adaptor sequences to trim more of adaptor from reads
  • 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[edit]

  • 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[edit]

  • 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[edit]

Get methylFreq & bed files from merged bam files[edit]