the difference between human and mouse wiggle files for uploading on UCSC

Question

[ashkan]

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!

Answer 1

[Satyajeet Khare]

The files are probably generated using non-UCSC GTF and Fasta file at the time of alignment (probably Gencode). You have three options.

1. You can make files compatible with UCSC browser,
2. Use the browser which is compatible with your files (in your case probably Ensembl), or
3. Use a browser such as IGV which ignores such errors. You can install it on your system and work offline.