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How to get lncRNA seqences from an annotation file?

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
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updated by Satyajeet Khare Satyajeet Khare • written by hydrinium.h2 • hydrinium.h2

try gffread

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

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written by Prasad Prasad

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

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written by Bruce • Bruce

1 answer

  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

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written by Satyajeet Khare Satyajeet Khare

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