Hisat2 output for stringtie
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Entering edit mode
6.1 years ago
Sam ▴ 150

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

hisat2 stringtie • 1.8k views
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Entering edit mode
6.1 years ago

Firstly, that is --dta-cufflinks and not --delta-cufflinks. Secondly, just use --dta/ --downstream-transcriptome-assembly option if you wish to use Stringtie.

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