Athurva Gore/LabNotes/2010-1-27: Difference between revisions

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{| {{table border=1}}
{| {{table border=1}}
| align="center" style="background:#f0f0f0;"|
| align="center" style="background:#f0f0f0;"|
| align="center" style="background:#f0f0f0;"|'''HL013 + HL025, SlideTrim5'''
| 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'', SlideTrim5'''
| align="center" style="background:#f0f0f0;"|'''HL013 + HL025 + ''HL034'', SlideTrim10'''
| align="center" style="background:#f0f0f0;"|'''HL013, HL025, ''HL034'', SlideTrim10'''
|-
|-
| dbSNP||align="right"|4071||align="right"|8643||align="right"|8093
| dbSNP||align="right"|4071||align="right"|8643||align="right"|8093
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|-
|-
| dbSNP%||align="right"|95.16%||align="right"|93.13%||align="right"|94.34%
| dbSNP%||align="right"|95.16%||align="right"|93.13%||align="right"|94.34%
|-
| CCDS Coverage (cov8, qual30)||align="right"|11260366||align="right"|19924839||align="right"|19866529
|-
| 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.
* Using the sliding trimmer with a 10 bp cutoff seems to fix the issue.

Revision as of 00:03, 28 January 2010

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:
HL013, HL025, SlideTrim5 HL013, HL025, HL034, SlideTrim5 HL013, HL025, HL034, SlideTrim10
dbSNP 4071 8643 8093
notdbSNP 207 638 486
dbSNP% 95.16% 93.13% 94.34%
CCDS Coverage (cov8, qual30) 11260366 19924839 19866529
Percent CCDS (cov8, qual 30) 39% 68.7% 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: