Athurva Gore/LabNotes/2009-9-8
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[edit]
Exome Sequencing[edit]
- Created script to trim first base off of reads.
- Did not affect as well as I had hoped.
PGP5 and PGP7[edit]
- After trimming first base and removing reads with SNPs in last 15 bp:
- PGP5: 11897 in dbSNP, 1752 not in dbSNP, (87.16% in dbSNP)
- PGP7: 13503 in dbSNP, 2613 not in dbSNP, (83.79% in dbSNP)
- Still very high rate of non-dbSNP.
- Found an error in the script! Was not actually tossing reads with SNPs in the last 15 bp. Whoops.
- Nevermind, error was not actually present.
- However, reran and trimmed first 2 bp and threw out last 15bp reads.
- Prefiltering:
- PGP5: 8977 in dbSNP, 793 not
- PGP7: 10373 in dbSNP, 1147 not
- Prefiltering:
- Still not very good. However, noticed that many reads seemed to have low quality...
- After coverage and quality cutoff:
- PGP5: 4361 hits, 215 misses (95.3% in dbSNP)
- PGP7: 5597 hits, 299 misses (94.9% in dbSNP)
- After coverage and quality cutoff:
- Much better, though fairly low coverage.
- This is due to the high number of lowquality reads (many reads that came out as %%%%%)