Kun:LabNotes/ExonomeSeq/2009-4-1: Difference between revisions

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===What is the level of representation bias?===
===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.
  [[Image:2009-03-30-AbsoluteCoverageDist.png|300px]] [[Image:2009-03-30-RelativeCoverageDist.png|300px]]
===What is the fraction of on-target reads?===
===What is the fraction of on-target reads?===
===What is the fraction of reads that came from linker sequences or capturing arms?===
===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?===
===How many SNPs were identified? What is the false positive rate?===

Revision as of 22:17, 1 April 2009

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?

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?