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Bamfile Coordinates

I blasted a gene sequence against a whole genome and found out that the subject start site:31636628 is higher than the subject stop site:31626793. I need the coordinates to excise a portion of a bamfile but since the subject start site is greater than the stop site, samtools reports invalid region. Can someone help me as to how best to specify these coordinates in my bamfile?

blast
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Kwame • Kwame

1 answer

IMHO, in BLAST start > end means that you matched the reverse complement sequence. Just swap the start and end position ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks Pierre. I have been struggle with this for sometime.

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written by Kwame • Kwame

Thanks Pierre. I have struggled with this for sometime

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written by Kwame • Kwame

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