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.