I am trying to make wiggle file to upload on UCSC. so far I have worked on human data. to do so I made a script in python using HTSeq. it has worked perfectly for human RNA-seq data. but now I am working on mouse data(RNa-seq). I used the same script to convert bam files to wiggle(strand specific files). I made it but this time when I tried to upload to the UCSC did nbot work and gave this error:
Error File '42_ag_+_.wig' - track load error (track name='ct_42025_6866'): Couldn't find size of chromosome 1 (note: chrom names are case sensitive)
I checked out the wig files I made for human and mouse, and in mouse there are some extera chromosomes like: GL456210.1, MG4151_PATCH etc. do you guys know what the possible problem is? and how I can resolve it? on UCSC I also change the genome from human to mouse(mm10). I asked this question before but did not get any reply!