Need Help, gap between two contigs formed by mapping

[ketan_bnf]

Hi all,

I have mapped reads to a ref seq using gsMapper and formed a contigs, now i want to extract & count length of the gap in reference sequence where no reads have mapped

Ref seq : AAGACTCGTGATCTGCTAGGCTCCTAAT
Alignme : AAGACTCGT---gap----AGGCTCCTAAT


How can i extract gap between two contigs using perl or bioperl?

Thanks.

[Soni]

Hi,
You can parse the headers of the 454AllContigs.fna to get the start and stop coordinates of the reference mapped by that particular contig. By a simple loop to substract the latter start position from the former stop position in Perl you can work out the coordinates for the unmapped regions.

Alternatively, use 454AlignmentInfo.tsv.

Hope this helps.

Soni