#126 illumina: care of PE contamination in mate-pair libraries

closed
None
5
2011-01-07
2010-11-19
Alexie
No

Hello

I have a 3kb Illiumina library which is contaminated with a higher than expected degree of PE reads (ca 250 bp). I've attempted to remove most of them up (it was about 50-60% of the reads) but some remain because the unitigger detects them

input: 14,800,608 pairs
project.008.libraryStats.log:
InsertSizes()-- lib 5 mean 238 stddev 77 samples 1015048

is there any way I can ask the overlapper to discard such reads? are there any other recommendations (sort of not using the data)?

thanks
a

Discussion

  • Brian Walenz

    Brian Walenz - 2011-01-07

    For the record, we have no good solution for this problem at the moment. You're better off filtering the reads from the input and starting the assembly over than trying to massage data out of gkpStore/ovlStore.

     
  • Brian Walenz

    Brian Walenz - 2011-01-07
    • assigned_to: nobody --> brianwalenz
    • status: open --> closed
     

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