Merge blastn hits sharing same subject
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Entering edit mode
4 months ago
vinicius ▴ 10

I have run blastn using a 300bp sequence as query (seq1), and got the following result:

# query  subject  sstart  send  length  gap
seq1  read1   200   350   150  0
seq1  read1   5000   5150   150  0
seq1  read2   700   1000   300   0

Is there any way that I can convert it, in a way that hits sharing the same subject sequencing are merged, and the distance between them are counted as gaps? Like this:

# query  subject  sstart  send  length  gap
seq1  read1   200   5150  300   4650
seq1  read2   700   1000   300   0

I am using BLASTn because I have +10k queries and +50k subjects. But if anyone knows any other program for such task, it would also be very helpfull.

Thanks,

alignment genome blast • 128 views
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