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mourisl / Rascaf

Scaffolding with RNA-seq read alignment
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Base-level error rate is high in assembly. Suggestions? #20

Closed chocotwig closed 1 year ago

chocotwig commented 4 years ago

Hi, I'm trying to apply Rascaf to an assembly that is unpolished and has high base level errors. I still want to try out Rascaf, and I was wondering if there are parameters we could tune to accept higher mismatch rates.

Thanks!

mourisl commented 4 years ago

Rascaf relies on the aligners and did not use mismatch rates after getting the alignment. You can adjust the parameters in RNA-seq aligner such as tophat, star or hisat for them to align reads with more mismatches.

chocotwig commented 4 years ago

Thanks!