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'''
|-
|-
| align = "right" | dbSNP||4071||8643||8093
| dbSNP||align="right"|4071||align="right"|8643||align="right"|8093
|-
|-
| notdbSNP||207||638||486
| notdbSNP||align="right"|207||align="right"|638||align="right"|486
|-
|-
| dbSNP%||95.16%||93.13%||94.34%
| 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

Latest revision as of 00:38, 28 January 2010

PGP Data[edit]

HL034 PGP5 Data[edit]

  • 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) 11,260,366 19,924,839 19,866,529
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[edit]

  • 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
Sample Reads Usable Reads Percent Usable CCDS Coverage (cov 8, qual 30) Percent CCDS Covered 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[edit]

  • 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