Question: How to get lncRNA seqences from an annotation file?
0
gravatar for hydrinium.h2
8 months ago by
hydrinium.h20 wrote:

Hi, I'm very new to bioinformatics in general so please excuse my ignorance. I'm trying to get sequences identified as long noncoding RNA in the mouse genome. I have a gtf file of only lncRNA annotations from Gencode, how do I get the actual sequences using this file? Any help would be greatly appreciated. Thank you.

rna-seq genome • 383 views
ADD COMMENTlink modified 8 months ago by Satyajeet790 • written 8 months ago by hydrinium.h20

try gffread

gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf

ADD REPLYlink modified 8 months ago • written 8 months ago by Prasad1.5k

are you analysing lncRNA from RNAseq? by using hisat or tophat?

ADD REPLYlink written 9 days ago by Bruce0
0
gravatar for Satyajeet
8 months ago by
Satyajeet790
Pune, India
Satyajeet790 wrote:
  1. Download reference genome in fasta format (same version as gtf file)
  2. Use bedtools getfasta as follows

    bedtools getfasta -fi reference_genome.fa -bed lncRNA.gtf -fo lncRNA.fa

ADD COMMENTlink modified 8 months ago • written 8 months ago by Satyajeet790
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 663 users visited in the last hour