Longshot on Iso-seq data #106
Description
Hi, thank you so much for the great tool.
I'm trying to apply longshot on long-read RNA-seq data (Iso-seq data from PacBio HiFi reads).
I ran the pipeline with default options and got ~30% reads assigned with HP tags (Is is true to assume HP:i:1 represents reads with REF SNPs and HP:i:2 with ALT SNPs?)
Do you have any recommendations to recover more reads?
I was wondering whether I should loosen
-I, --max_cigar_indel <int> Throw away a read-variant during allelotyping if there is a CIGAR indel
(I/D/N) longer than this amount in its window. [default: 20]
since the RNA-seq reads CIGAR skips large introns.
Thank you so much for your kind help.