Kun:LabNotes/ExonomeSeq/2009-4-1: Difference between revisions
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===What is the fraction of on-target reads?=== | ===What is the fraction of on-target reads?=== | ||
*Read mapping using Soap2 with the default setting. | |||
**19,132,747 total reads. | |||
**15,217,219 mapped. | |||
*I used this [[Media:seqCoverage.txt |Perl script]] to generate the following statistics: | *I used this [[Media:seqCoverage.txt |Perl script]] to generate the following statistics: | ||
Genome covered(bps) Sequenced(bps) | Genome covered(bps) Sequenced(bps) |
Revision as of 23:05, 11 May 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?
- Read mapping using Soap2 with the default setting.
- 19,132,747 total reads.
- 15,217,219 mapped.
- 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?
- I've tried both Maq and Soap on either the full genome template or the captured targets only. SNP calling was based on the minimal sequencing coverage of 8x and the minimal quality score of 30.
Full genome Targets only Maq 10,655 10,202 SOAP 15,485
File:Comparison of SNP calling strategies.png