Question: long non-coding RNA in genome guided assembly
0
gravatar for nabiyogesh
4 months ago by
nabiyogesh70
South Korea
nabiyogesh70 wrote:

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 • 140 views
ADD COMMENTlink modified 4 months ago by liuwei0 • written 4 months ago by nabiyogesh70
0
gravatar for liuwei
4 months ago by
liuwei0
Shanghai
liuwei0 wrote:

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.

ADD COMMENTlink written 4 months ago by liuwei0

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

ADD REPLYlink written 4 months ago by nabiyogesh70

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

ADD REPLYlink written 4 months ago by liuwei0
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