Question: Hisat2 output for stringtie
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gravatar for Sam
20 months ago by
Sam140
Sam140 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 • 752 views
ADD COMMENTlink modified 20 months ago by lakhujanivijay5.1k • written 20 months ago by Sam140
0
gravatar for lakhujanivijay
20 months ago by
lakhujanivijay5.1k
India
lakhujanivijay5.1k 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 20 months ago • written 20 months ago by lakhujanivijay5.1k
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