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

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===Was the library construction successful?===
===Was the library construction successful?===
It seems pretty good. Here is the distribution of reads that mapped to the same location.
It seems pretty good. Here is the distribution of reads that mapped to the same location.
[[Image:2009-03-30-clonality_check.png|300px]]
[[Image:2009-03-30-clonality_check.png|500px]]


===What is the level of representation bias?===
===What is the level of representation bias?===

Revision as of 22:16, 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?

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?