1
$\begingroup$

I was able to get the exons of a particular gene as a fasta file from the NCBI genome viewer. As for introns I only found a bed file that showed where the intron starts and ends, along with its direction. What tool do I use to get the exact sequence of these 11 introns using this bed file? And is there a more direct way? Thank you.

$\endgroup$

1 Answer 1

1
$\begingroup$

First I edited the Chromosome column of the bed file from ncbi, because it contained the accession number instead of the chromosome. Then I used the getfasta tool of the bedtools utility.

bedtools getfasta -fi input_genome_file.fa -fo output.fa -bed bed_file

The output contained the introns in the format I wanted. If anybody had a better way, feel free to post.

$\endgroup$
2
  • $\begingroup$ Hi @venkateshwar thank you for sharing this information. Could you just confirm that this is the answer to the question you posted (it looks like it)? $\endgroup$
    – M__
    Jan 16, 2023 at 18:00
  • $\begingroup$ @M__ Ok I will. $\endgroup$ Jan 17, 2023 at 5:21

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.