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  • #1

    CIGAR Format and DEGSEQ

    Hi Everyone. I'm having difficulty interpreting CIGAR output from SSAHA2. Could anyone please help me interpret the following CIGAR output?:

    cigar::50 ERR023002.2 31 17 - Tb927_11_03_v4 233403 233417 + 15 M 15

    Also, I need to filter the reads by CIGAR score, so which one is considered to be the CIGAR score?

    Finally, I want to run these on DEGseq, which takes only bed files. Is there any utility out there that converts CIGAR to BED?

    Thank you!
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