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

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* 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.

Revision as of 19:50, 8 September 2009

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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.