Kun:LabNotes/ExonomeSeq/2009-4-1

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Data analysis of shotgun sequencing data

  • Two libraries were made by Alice. The capturing reactions were done with Jan09 #1-3 probe set (150k) on PGP1.
  • s3 (PGP1-CTRL): 9707995 raw reads, 40bp, 7655774 (79%) mappable (SOAP2 to hg18)
  • s4 (PGP1-Shaked): 9424752 raw reads, 40bp, 7561445 (80%) mappable (SOAP2 to hg18)

Questions to answer

Was the library construction successful?

It seems pretty good. Here is the distribution of reads that mapped to the same location. File:2009-03-30-clonality check.png

What is the level of representation bias?

What is the fraction of on-target reads?

What is the fraction of reads that came from linker sequences or capturing arms?

How many SNPs were identified? What is the false positive rate?