This is a test version of Biostars. For the public version, visit https://www.biostars.org.
long non-coding RNA in genome guided assembly

I have mapped pair end Illumina read to genome using Hisat2 and further assembled into transcripts using StringTie. I am wondering whether these assembled transcripts contains long non-coding RNA or not.

If Yes, then please suggest how can I remove these long non-coding RNA.

Thanks in advance.

rna-seq
• 1,747 views • link
updated by liuwei • liuwei • written by Bioinfonext Bioinfonext

1 answer

When you use StringTie to asemble, the gtf file contain mRNA and non coding RNA.So,filt the non coding RNA in the gtf file and the result will only be protein coding transcrpt.

• 0 views • link
written by liuwei • liuwei

Please suggest the tool that can remove non-coding RNA from gtf file.

• 0 views • link
written by Bioinfonext Bioinfonext

you should understand the feature of GTF file and use shell command can to that( google 'shell grep')

• 0 views • link
written by liuwei • liuwei

Log in to answer this question.

More posts like this