How to get the nucleotide sequence through ORF information?
I have a file with ORF information, including the start position and end position on the chromosome. At first I wanted to create a bed file, and then use the getFastaFromBed of bedtools to get the sequence.
But I found that the sequence obtained in this way includes introns, which makes it impossible for me to predict the amino acid sequence later. I have GTF files containing exon information, but it is difficult for me to process these ORFs in batches. Is there any tool or code that can help me get the nucleotide sequence with intron removal?
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