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Question: Filter Pileup Error in SAMtools
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gravatar for john.doyle
2.9 years ago by
john.doyle • 0
john.doyle • 0 wrote:

Hi,

I am a new user to Galaxy and am having trouble with a filter pileup error. The error message I am receiving is as follows: "Coverage column 4 contains non-numeric values". I tried converting the Mpileup file to pileup format, but pileup filter still did not work. Any thoughts on where I am going wrong?

Thanks,

John
software error galaxy samtools • 731 views
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modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by john.doyle • 0
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gravatar for Jennifer Hillman Jackson
2.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello John,

What output setting for Mpileup are you using? The default should work with the filter. Other options will not due to format incompatibilities. The data examples on each tool form has examples for comparison.

We can troubleshoot more if you are still not sure of the settings and the output each produce versus your data. Send in a bug report from the error dataset (via green bug icon). Please make certain that all input and error datasets are undeleted.

(This assumes you are working at http://usegalaxy.org. If not, maybe see if you can reproduce there- that can be useful information if we need to expand the troubleshooting for a local or cloud).

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k
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