I am using Galaxy on a PC. My peak calling software is a PC based program built into DNAstar. Unfortunately it does not have a way to concatenate the called peaks into a single bigwig file. The output is single chromosome specific wig files. Is there a way in the Galaxy wig to bigwig tool to have it combine multiple wig files into one bigwig file? I also do not have access to a Unix machine or a Mac. I did a test using EM editor and found that I can manually combine these files . I just need to re-enter by hand a line break b/w Chromosome track info. The files become huge and I am not sure that I can combine all the mouse chromosome wig files and still be allowed to upload it to Galaxy. Having a single bigwig file for all my called peaks will enable me to generate a single custom track in the USCS browser. I need to make six of these custom tracks to identify peaks where our molecule of interest is contacting the genome.
Thanks for everyone's thoughts on how to do this task.