I'm currently processing ChIP-seq data from C.elegans.
I've used data from GEO which I processed this way:
sra -> fastq (fastq-dump) -> sam (bwa) -> bam (samtools view) -> bed (bedtools bamtobed)
However I noticed chromosome names were in RefSeq format:
NC_003282.8 9767072 9767122 NC_003284.9 7940872 7940922 NC_003284.9 112717 112746
I would like to get "standard" chromosome names (eg chr1, chr2...). Does one of the tools I used so far allows that? If not, is there a way to convert bedfiles, or at least some kind of conversion table?
Thanks a lot!