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Question: Circster problem can't create visualisation: 1 is not found in chromosome sizes file, or nothing happens!
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gravatar for c.proukakis
2.8 years ago by
c.proukakis • 0
c.proukakis • 0 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 • 547 views
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modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by c.proukakis • 0
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gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k
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