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?

It is slightly higher than the bias in end-sequencing analysis, but not too much. The library construction could be improved. Library-free sequencing would be better.

 File:2009-03-30-AbsoluteCoverageDist.png File:2009-03-30-RelativeCoverageDist.png

What is the fraction of on-target reads?

  • I used this Perl script to generate the following statistics:
                       Genome covered(bps)   Sequenced(bps)      
   Mapped reads:	44,333,324	      608,688,760
   On-target reads:	15,064,164	      499,303,049 (33x)  82%
   Near-target	reads:	 4,005,655	      93,306,387  (23x)  15%

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?