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{{ AGLabEntry|2009-9-4|2009-9-9 }} =Exome Sequencing= * Created script to trim first base off of reads. ** Did not affect as well as I had hoped. ==PGP5 and PGP7== * 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 * 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) * '''Much better, though fairly low coverage.''' * This is due to the high number of lowquality reads (many reads that came out as %%%%%)
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