How to get lncRNA seqences from an annotation file?

Question

[hydrinium.h2]

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.

[Prasad]

try gffread

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

[Bruce]

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

Answer 1

[Satyajeet Khare]

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