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Aligning Reads with Overhangs on the Ends (Edges) of Reference Contigs or Scaffolds
Hi all!
Does anyone know any option in any software that could say:
"In the case a read aligns to the beginning or end of a contig/scaffold of the reference but has an overhang, as long as the matching part is longer than some threshold, do not think of the overhang as mismatch, and calculate mapping just based on the part that actually aligns"
A short example:
reference contig= AAGCTTCACACATATAT
read= CACGTATGAAAGCTT
So I want to keep these reads, but the mismatch caused by the overhang causes these reads to be excluded from the alignment.
I have short contigs in the reference and short reads, and this gives me very bad alignment results at the beginnings and ends of the reference contigs.
Many Thanks!
Does anyone know any option in any software that could say:
"In the case a read aligns to the beginning or end of a contig/scaffold of the reference but has an overhang, as long as the matching part is longer than some threshold, do not think of the overhang as mismatch, and calculate mapping just based on the part that actually aligns"
A short example:
reference contig= AAGCTTCACACATATAT
read= CACGTATGAAAGCTT
So I want to keep these reads, but the mismatch caused by the overhang causes these reads to be excluded from the alignment.
I have short contigs in the reference and short reads, and this gives me very bad alignment results at the beginnings and ends of the reference contigs.
Many Thanks!