Dinh 2011/NOTES/2011-12-22

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Revision as of 19:58, 22 December 2011 by >Dinh
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Yi Zhang Lab (UNC) 24 ChIP/DIP Data

Analysis of enrichment in repeats

PE Data

  • FastqC on 100,000 reads
READ1 (Indx15)
File:YiZhang 24ChIP PE read1.png
READ2 (Indx2)
File:YiZhang 24ChIP PE read2.png
  • Trimming 5 bp from 5' of Read1 and 20 bp from 5' of Read2
  • Sequence size is 300-600 (Alan's gel cut labnote)
  • Mapping procedure from BWA's manual:
bwa aln ref.fa -b1 reads.bam > 1.sai 
bwa aln ref.fa -b2 reads.bam > 2.sai 
bwa sampe ref.fa 1.sai 2.sai reads.bam reads.bam > aln.sam
  • I expect that if the paired read flank onto repeats, one read will map uniquely while another will be mapped non-uniquely. BWA sampe will find the best unique mapping for the pair.
  • Trimming with BWA is most based on quality score, according to the manual,
-q is : Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0]
Here is a nice diagram explaining this from SeqAnswers:
File:BwaTrimming.jpg
Thus I will use -q 20 for trimming.
  • I will map all the fastq first using:
bwa aln -l 28 -k 3 -t 16 -q 20 -I /media/disk-1/Dinh_Scratch/mm9Annotations-iGenomeUCSC/BWAIndex/mm9 
    • checked that quality values are in ASCII-64!
  • Ran mapping..
 15.7% of bases are trimmed for Read 1