convert bed file to fasta file

Question

[hana]

Hi

I have the transcript.gtf file from cufflinks. I would like to identify novel long non_coding RNA using lncRScan.

I need to convert the gtf file to bed file and bed file to fasta file.

any suggestion would be appreciated.

Thanks

Answer 1

[poisonAlien]

gtf to bed

getFastaFromBed

Answer 2

[jlncrnt]

Based on this comment, if you want a direct gtf/gff -> fasta conversion:

gffread your_transcripts.gff -g genomic_reference.fasta -w your_transcripts.fasta​

Answer 3

[Alex Reynolds]

Here's a one-liner via gtf2bed and bed2faidx:

$ gtf2bed < annotations.gtf | bed2faidx > annotations.fa

You'll need samtools and samtools-indexed FASTA files to run bed2faidx.