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%