long non-coding RNA in genome guided assembly

Question

[Bioinfonext]

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.

Answer 1

[liuwei]

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.

[Bioinfonext]

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

[liuwei]

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