gtf assembled using stringtie has lines missing strand info

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq

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gtf assembled using stringtie has lines missing strand info #322

Open linzhangTuesday opened 3 years ago

linzhangTuesday commented 3 years ago

Hi I used stringtie to assemble a new transcriptome and merge with a reference one.

The output gtf has ~30 lines without strand info in field 7 , compared to ~360k lines are + and - respectively. The downstream software is complaining about "Invalid strand" for those lines missing strand info while parsing the gtf file. Those lines all look like new-assembled with only "MSTRG.#".

Please let me know if there are any suggestions.Thanks in advance!

ghost commented 3 years ago

I have the same issue, in some of the transcripts my strand is simply "." Did you solve this? Thanks!

YIGUIz commented 2 months ago

single exon transcripts will have the problem. https://github.com/gpertea/stringtie/issues/20