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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Transcripts of only one exon #261

Closed reutnuri closed 4 years ago

reutnuri commented 4 years ago

Hi,

I used STAR for mapping short reads to genome. I ran StringTie with the following command: stringtie sorted_Aligned.out.bam -p 20 -A stringtie_run5.tab -o stringtie__5.gtf -l new.strg -p 12 -j 2

My output GTF file contains only transcripts of a single exon. Checked it in IGV and there are adjacent exons that could be joined to transcripts.

Can anyone help me understand what went wrong in my run?

Thanks!!

gpertea commented 4 years ago

I do not have experience with STAR, I hope you made sure to run it with the appropriate options for RNA-Seq data and suitable for transcript assembly (there should be something in the STAR manual about what options to use for Cufflinks or transcript assembly in general). Also, do you actually see intron-spanning read alignments in IGV ? You mentioned you see that there are adjacent exons where reads were mapped, but are there read alignments actually spanning those multiple exons, with actual intron gaps in the alignment?

reutnuri commented 4 years ago

Thanks for your quick response! Yes, I see reads spanning over exons. However, I did not used the Cufflinks option, I will try to run it again and see if it solves the problem. Will update if it solves the problem. Thanks again :)

reutnuri commented 4 years ago

It was indeed an issue with Star for preparing the DB for Cufflinks. Many thanks!