Athurva Gore/LabNotes/2009-9-8: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Ajgore
>Ajgore
 
(One intermediate revision by the same user not shown)
Line 10: Line 10:
* Still very high rate of non-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.
* Found an error in the script!  Was not actually tossing reads with SNPs in the last 15 bp.  Whoops.
** Fixed, modified script to trim the first two bp, reran scripts.
** 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 %%%%%)

Latest revision as of 20:13, 8 September 2009

Navigation[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
  • 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 %%%%%)