Dear All

I used histat2 to report alignment with --delta-cufflinks flag (tailor for cufflinks) but I want to use that sorted bam files to assemble by Stingtie, according to the hisat2 manual this flag report alignment tailored specifically for Cufflinks, in addition to what hisat2 does. so is it wise to use the that sorted bam files for stringtie or it may produce some false positive/negative results?

Thanks