gtf assembled using stringtie has lines missing strand info

[linzhangTuesday]

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]

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