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Question: Ngs Sam Tools: Filter Pileup Tool Not Working
1
gravatar for Lanelle Oni Edwards
6.0 years ago by
Lanelle Oni Edwards • 50
Lanelle Oni Edwards • 50 wrote:
Hello, I am currently using galaxy main to run a filter pileup on datasets that used the generate pileup tool. The filter pileup function is not recognizing any of my generate pileup datasets in the drop-down box so I cannot even execute the job. I think there may be a problem with this tool. I would greatly appreciate any help or an update as to when this tool will be functioning again. Thank You, Lanelle Edwards
galaxy • 1.2k views
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modified 6.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.0 years ago by Lanelle Oni Edwards • 50
1
gravatar for Jennifer Hillman Jackson
6.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Lanelle, My initial guess is that the datatype is not set as "pileup" for your dataset - a standard, 6 column pileup format dataset. Perhaps you used the option to generate a "consensus pileup" with 10 columns? And so the output is labeled as tabular format? If so, you can cut the first 3 columns and last 3 columns out, paste them together, and assign the format "pileup" to use with the downstream filter tool. Tools to do the Cut/Paste are in the group 'Text Manipulation'. If the datatype does not explain the issue, please let us know and we can look into this more. From a quick test I didn't find anything unusual, but of course we would want to track down any potential bugs, Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.0 years ago by Jennifer Hillman Jackson ♦ 25k
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