Question: Hisat2 output for stringtie
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gravatar for Sam
3 months ago by
Sam100
Sam100 wrote:

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 • 204 views
ADD COMMENTlink modified 3 months ago by Vijay Lakhujani3.6k • written 3 months ago by Sam100
0
gravatar for Vijay Lakhujani
3 months ago by
Vijay Lakhujani3.6k
Vijay Lakhujani3.6k wrote:

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

ADD COMMENTlink modified 3 months ago • written 3 months ago by Vijay Lakhujani3.6k
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