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.
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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.
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$\begingroup$ 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__ ♦Commented Jan 16, 2023 at 18:00
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