search

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
361 stars 76 forks source link

Segmentation fault (core dumped) and problems of gene orientations #406

Open Cesnl opened 10 months ago

Cesnl commented 10 months ago

When I use the -mix parameter, I consistently encounter an error message that says "Segmentation fault (core dumped)." However, when I run StringTie separately with either short read BAM or long read BAM files, I don't receive any errors. What could be the reason for this? Additionally, I'd like to inquire why the gene orientations represented as '+' and '-' in the output GTF file from StringTie using short read BAM files are completely opposite to those in the reference annotation GTF.

Cesnl commented 10 months ago

Looking forward to your response. Thank you very much.

YIGUIz commented 3 months ago

hi, I met the same error. Did you solve this problem? Can you give me some advice?

the parameters are the following:

stringtie -o Mammary.Gland_3_mix.out.gtf --mix -p 12 --rf Mammary.Gland_3Aligned.sortedByCoord.out.bam Mammary.Gland_3.sorted.bam

Thank you for your help!

gpertea commented 3 months ago

Could you please try to the latest version (v2.2.2) just posted a couple of days ago, and if you still encounter the error it would be great if you can provide some example data so we can look into to the issue more closely. Thanks!