I have a fasta file rn4.fa with the rat genome and also a fai file rn4.fa.fai which I generated with samtools faidx. I want to extract fasta from bed like this (below), but I get an error message "could not stat file".
I am using fastaFromBed Version: v2.16.1
I am pretty much stuck here - anything I can do to get fastaFromBed working?
Thanks!
Code:
fastaFromBed -name -fi ../rn4/rn4.fa -bed foo.bed -fo bar.fa could not stat file../rn4/rn4.fa
I am pretty much stuck here - anything I can do to get fastaFromBed working?
Thanks!
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