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  • aleferna
    Senior Member
    • Sep 2009
    • 121
    #1

    maq2sam-long eats first letter

    Hi, I'm running maq2sam-long and it seems to be eating the first N letters of my reads which is a big pain as I'm trying to compare mapping quality between different algorithms to map a solexa run. Any ideas or patches available?

    All read id's should start with MID10

    ID10_6:1:11989:5823:TGACCA_1_M76-97 16 chr10...
    D10_6:1:11988:14238:TGACCA_1_M72-97 16 chr1...
    ID10_6:1:11980:7951:TGACCA_1_M76-97 16 chr6...
    ID11_6:1:1198:12269:ACAGTG_1_M24-43 0 chr18...
    6:1:1198:12269:ACAGTG_2_M0-42_M0-18 16 chr7...
    ID12_6:1:11989:4489:GCCAAT_2_M80-97 0 chr2...
    MID12_6:1:11982:3900:GCCAAT_2 16 chr13...
    MID13_6:1:11982:9036:CAGATC_1 0 chr10...
    Tags: None
    • aleferna
      Senior Member
      • Sep 2009
      • 121
      #2
      sorry should start with MID10, MID11, MID12, etc, etc, etc

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