I have received a set of BAM files generated from RNAseq (PE100) of the opossum, MonDom5.
When I generate Bedgraph gene coverage files of this data, column 1 lists only a number without the chr designation, i.e., "1" not "chr1". I think this a problem with the BAM files, which do not have the tabular layout of our files from other species. Is there an easy way to fix the BAM files?
Alternatively, is there an easy way to rewrite column 1 in the Bedgraphs?