search

jeffdaily / parasail

Pairwise Sequence Alignment Library
Other
243 stars 34 forks source link

Different gap penalty for template and query #79

Open Nil-Fernandez-Lojo opened 4 years ago

Nil-Fernandez-Lojo commented 4 years ago

Hi Jeff,

First of all, thank you for this amazing software!

I am trying to use your code for an assignment for university where I need to code a RNA to DNA mapper. I get a FASTQ file containing data from RNA-seq and I need to map the reads to a reference genome. When I get a partial map between my read and the genome (using a FM index), I use your aligner to tolerate insertions and deletions and it works very well. So thank you for that!

I was also interested in using your library to match reads that were spliced. However to do so, the aligner should tolerate long insertions in the read but no deletions (or at most few deletions). This would be possible if I could use a different gap penalty for the template and the query. I think that adding that feature to your aligner (if it is possible) would extend even more its possible applications.

Thank you for your help,

Nil

y9c commented 2 years ago

Looking forward to have this feature.