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