Input zipped fastq or aligned bam file for Isoquant

[Vibha1277]

Hi Team,
I have pacbio .ccs reads for isoseq count and then DEG analysis.
Should input isoseq fastq.gz file go through trimming the primers or adapter removal and or polyA tail removal first begore running for isoseq count?

Thanks and Regards,
Vibha

[andrewprzh]

Dear @Vibha1277

Removing adapters and primers would be nice, but it's better to keep polyA tails since IsoQuant relates on those when detecting transcript end sites.

Best
Andrey