bedtools getfasta skipping problem

[mharoun20]

Hi,
I am trying to implement the model following the tutorials. When I try top convert the bed file to FASTA format using getfasta, I get the error "Feature xxx beyond the length of xxx size (8 bp). Skipping. " I read that a solution method is to make use of contig file that I do not think is provided.

Any tips/guidance how to solve this?

Best,
Mahmoud

[davek44]

Hi Mahmoud, which tutorial are you working through?

You might consider moving to Basenji codebase, which I'm much more easily able to maintain these days. I have the Basset model exemplified here: https://github.com/calico/basenji/tree/master/manuscripts/basset