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  • #1

    Representation of sequencing error in SAM

    Hi,
    I'm aligning solid reads using BWA and I'm trying to differentiate between actual mismatches and sequencing errors. Do reads with sequencing errors just fail to align or is there a special representation for them in the SAM output?
    I see that SHRIMP does give a sequencing error indication in it's results.

    Thanks!
    Temima
    Tags: bwa, sequencing error, solid reads
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