Aligning Reads with Overhangs on the Ends (Edges) of Reference Contigs or Scaffolds

Question

[FatihSarigol]

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=                  AGAGAGAGTTTCCCGAGTATATAGAGACACAGAGTGGTGAGGAT
READ WITH OVERHANG=    TTATAGGTTCCGAGAGAGAGTTTCGC
another read=                                   CGAGTATATAGAGACACA
READ WITH OVERHANG=                                            ACAGAGTGGTGAGGGTGGAGAT
ALIGNED READ WITH 2 SNPS=          AGAGAGAGTTTCGCGAGTATATAGAGACACAGAGTGGTGAGGGT

Many Thanks!

[EVR]

Hi Durham,

Such type of reads must be filtered out in the unaligned reads. You can start fishing from there and that is the best starting point.

[FatihSarigol]

Hi, thanks, I dont want to filter them out, I want to keep them. Otherwise the mismatch caused by the overhang already excludes these reads 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. Thanks