search

alexdobin / STAR

RNA-seq aligner
MIT License
1.77k stars 495 forks source link

Aligning reads to transcripts #2141

Open sagnikbanerjee15 opened 1 month ago

sagnikbanerjee15 commented 1 month ago

Hello,

I have a set of reads sequenced on PacBio. I wish to align those to a transcriptomic reference that contains sequences highly similar to one another (some have only 3-6 nucleotides of difference). There is no genome so I cannot allow for a spliced alignment. I set the alignIntronMax and alignIntronMin to 0 but the final alignments still contain some splices. How do I turn it off entirely? Also is there a way I can generate an expanded cigar with = and X?

Thanks. Sagnik