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=PGP Data= ====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? ====New PGP Coverage Summary==== * We can use these new data sets to obtain new coverage statistics as well. ** Uses data from previous table for PGP1-6, PGP8, PGP10 (''add link''), sliding trimmer 5 ** Uses data from previous table for PGP7 and PGP9 (''add link''), sliding trimmer 10 ** Uses PGP4, PGP6, and PGP10 old data (from before last September; probably only reliable good data from that time period) ** Uses HL034 PGP5 data with sliding trimmer 10 {| {{table border=1}} | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Reads''' | align="center" style="background:#f0f0f0;"|'''Usable Reads''' | align="center" style="background:#f0f0f0;"|'''Percent Usable''' | align="center" style="background:#f0f0f0;"|'''CCDS Coverage (cov 8, qual 30)''' | align="center" style="background:#f0f0f0;"|'''Percent CCDS Covered''' | align="center" style="background:#f0f0f0;"|'''dbSNP %''' |- | '''PGP1'''||73,656,659||52,445,891||0.71||22,543,941||'''78%'''||95.22% |- | PGP2||13,777,534||8,201,178||0.6||9,964,899||35%||95.26% |- | PGP3||19,642,850||12,512,635||0.64||11,716,319||40%||94.54% |- | '''PGP4'''||101,486,098||57,569,270||0.57||21,358,854||'''74%'''||94.42% |- | '''PGP5'''||50,460,039||28,632,469||0.65||19,866,529||'''69%'''||94.34% |- | '''PGP6'''||86,066,955||58,086,066||0.67||21,177,467||'''73%'''||94.14% |- | PGP7||28,619,340||15,398,503||0.54||12,535,785||44%||94.16% |- | '''PGP8'''||116,237,040||61,363,238||0.53||20,930,980||'''72%'''||94.60% |- | '''PGP9'''||117,277,366||55,399,638||0.47||20,677,998||'''72%'''||94.47% |- | '''PGP10'''||55,310,684||35,456,916||0.64||19,759,504||'''68%'''||88.97% |} ====PGP2, PGP3, PGP7==== * Have new data from HL035 for these sets ** Currently mapping two lanes of PGP2 and two lanes of PGP3 ** Still need to map the one lane of PGP7; make sure to use slidingTrimmer 10 * Can then merge in, see how many bases we have
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