Question: Hisat2 output for stringtie
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gravatar for Sam
8 months ago by
Sam120
Sam120 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 • 447 views
ADD COMMENTlink modified 8 months ago by lakhujanivijay4.3k • written 8 months ago by Sam120
0
gravatar for lakhujanivijay
8 months ago by
lakhujanivijay4.3k
India
lakhujanivijay4.3k 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 8 months ago • written 8 months ago by lakhujanivijay4.3k
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