text: user9089: 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.
  
  user9089: 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.
  
original_text: 9089: <p>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.</p>
   9089: <p>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.</p>
  <p><code>bedtools getfasta -fi input_genome_file.fa -fo output.fa -bed bed_file</code></p>
  <p>The output contained the introns in the format I wanted.
  If anybody had a better way, feel free to post.</p>
  