Question: the difference between human and mouse wiggle files for uploading on UCSC
gravatar for ashkan
3.4 years ago by
ashkan110 wrote:

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!

rna-seq • 1.2k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by ashkan110
gravatar for Satyajeet Khare
3.4 years ago by
Satyajeet Khare1.5k
Pune, India
Satyajeet Khare1.5k wrote:

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.
ADD COMMENTlink written 3.4 years ago by Satyajeet Khare1.5k
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