running with --dta did not produce XS tag

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq

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running with --dta did not produce XS tag #181

Closed tenger-github closed 6 years ago

tenger-github commented 6 years ago

Dear , When I ran Hisat2 (version: 2.1.0) with --dta ( --downstream-transcriptome-assembly OR --dta-cufflinks), there was no XS tag in output file. I did not know how to fix it. Thank you very much!

gpertea commented 6 years ago

This seems very unlikely -- though I guess it's possible to happen if there were no spliced alignments at all (which would be strange). In any case, this seems to be an aligner (or aligner usage) issue (HISAT2), not a StringTie issue..