while creating an index for the bovine genome with STAR, the process fails because the chromosome names in the annotation file (Bos_taurus.UMD3.1.87.gtf) are incompatible with the ones in the reference file (UMD3.1_chromosomes.fa) (e.g. for chromosome "10" vs "gnl|UMD3.1|GK000010.2 Chromosome 10 AC_000167.1", both should be "10").
Apparently, the solution is to change the names in the reference file. Could you suggest a tool that does this for me or a "one liner" that can transform the names into the chromosome number?
And also, would this affect downstream processing of my results?
I have searched through other threads and couldn't find a better answer than the one given here: Renaming Entries In A Fasta File But it renames chromosomes names in the reference file based on the order they appear.