Question: Circster problem can't create visualisation: 1 is not found in chromosome sizes file, or nothing happens!
0
gravatar for c.proukakis
22 months ago by
c.proukakis0 wrote:

I am a total novice, and hoped that circster would be the answer to my prayers.

My PE human WGS low coverage bam files come up as error  1 is not found in chromosome sizes file

A human mate pair WGS simply does nothing- it goes yellow while it is trying, and then grey with no output 

 

anu suggestions very welcome

 

 

 

 

 

 

software error circster • 355 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson23k • written 22 months ago by c.proukakis0
1
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Double check that the chromosome identifiers in the data are exactly the same as in the reference genome. A mismatch could trigger this type of problem.

How to detect and correct mismatch reference genome mismatch issues: https://wiki.galaxyproject.org/Support#Reference_genomes

If this doesn't work, test to see that the behavior is reproducible at http://usegalaxy.org (if working elsewhere). If so, create a share link from the history and visualization and email those along with a link to this post to galaxy-bugs@lists.galaxyproject.org for troubleshooting.

Thanks, Jen, Galaxy team

 

ADD COMMENTlink written 22 months ago by Jennifer Hillman Jackson23k
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