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====HL034 PGP5 Data==== * Got some new PGP5 data from HL034 ** Dr. Zhang tried to map it; ended up with a very low dbSNP percentage (~70%) * Can we fix it with some trimming? ** Tried sliding trimmer 5 and 10 ** Merged it into the previous data ** Got the following results: {| {{table border=1}} | align="center" style="background:#f0f0f0;"| | align="center" style="background:#f0f0f0;"|'''HL013, HL025, SlideTrim5''' | align="center" style="background:#f0f0f0;"|'''HL013, HL025, ''HL034'', SlideTrim5''' | align="center" style="background:#f0f0f0;"|'''HL013, HL025, ''HL034'', SlideTrim10''' |- | dbSNP||align="right"|4071||align="right"|8643||align="right"|8093 |- | notdbSNP||align="right"|207||align="right"|638||align="right"|486 |- | dbSNP%||align="right"|95.16%||align="right"|93.13%||align="right"|94.34% |- | CCDS Coverage (cov8, qual30)||align="right"|11,260,366||align="right"|19,924,839||align="right"|19,866,529 |- | Percent CCDS (cov8, qual 30)||align="right"|39%||align="right"|68.7%||align="right"|68.5% |} * Using the sliding trimmer with a 10 bp cutoff seems to fix the issue. * The dbSNP percentage is still very close to the one found in the other libraries. * Not sure what happened ** Same library works earlier with sliding trimmer 5, but now requires sliding trimmer 10? ** Something to do with flowcell?
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