Hi,
I had to extract 100kb flanking sequences of a list of RNA sequences from the whole genome. For this, I used bedtools flank to extract the genomic coordinates of the flanking regions of RNAs. But then when I try to extract the sequences in FASTA format using bedtools getfasta command, the analysis stops where the start coordinate is greater than end for a particular gene id. The error message is this Error: cannot construct subsequence with negative offset or length < 1
Bedtools doesn't further extract sequences for the downstream gene ids and stops analysis at that point. Is there any way to ignore coordinates where start > end, and to return sequences in FASTA format for the remaining gene ids?
Any help will be much appreciated. Thank you.
Your BED files must obey the BED conventions, means start < end and zero-based.