Question: How to get lncRNA seqences from an annotation file?
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gravatar for hydrinium.h2
2.3 years 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 • 934 views
ADD COMMENTlink modified 2.3 years ago by Satyajeet Khare1.3k • written 2.3 years ago by hydrinium.h20

try gffread

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

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Prasad1.5k

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

ADD REPLYlink written 19 months ago by Bruce0
0
gravatar for Satyajeet Khare
2.3 years ago by
Satyajeet Khare1.3k
Pune, India
Satyajeet Khare1.3k 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 2.3 years ago • written 2.3 years ago by Satyajeet Khare1.3k
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