Question: Subtraction between datasets not showing chromosome number in bed format and is instead showing + signs.
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cmezator • 10 wrote:
Hello,
Whenever I try to subtract datasets, I get (+) signs instead of the chromosome number in the BED format. Sometimes when I subtract datasets, the "chr" column is correctly displayed, however in some instances I just get a series of + signs. I am trying to subtract the simple repeats dataset from the mouse (mm10) genome from the dataset that shows the difference between the intergenic regions and the repeatmasker.
Thanks,
Carlos
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modified 2.2 years ago
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Jennifer Hillman Jackson ♦ 25k
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2.2 years ago by
cmezator • 10
Hello,
The tool Join, Subtract and Group > Subtract Whole Dataset from another dataset does not manipulate the data. Lines between datasets are directly compared. If a line contains unexpected data, it was present in the original inputs.
This assumes there is not a problem with the tool. At this time, none are known. Please check the outputs against the original input first. If you discover a problem (lines in the output that are NOT present in the inputs), please share the history, leave all datasets in the analysis undeleted - including any test datasets generated, and send that shared history link along with a link to this Biostars post to galaxy-bugs@galaxyproject.org.
How to share a history: https://wiki.galaxyproject.org/Learn/Share
Common troubleshooting & data investigation methods/tools: https://wiki.galaxyproject.org/Support#Troubleshooting_tool_errors_-_Review_THIS_before_submitting_bug_reports
Best, Jen, Galaxy team
Ah, just saw that you are using the tool Operate on Genomic Intervals > Subtract instead.
I am going to leave the above posted, but moved to a comment.
Please instead just share the history as described and we can review what the issue is. Please note that http://usegalaxy.org is undergoing some quick admin changes right now - so some functions like sharing may be difficult (result in a Galaxy could not be reached message). Wait a bit and it is expected to clear.
Hey Jennifer,
Here is the link to the history I am working on: https://usegalaxy.org/u/carlostorres/h/galaxy-101-2016 Best,
Carlos
There are some items from the history that are correctly displayed but on some datasets like the Neutral Regions one, just has a series of + signs on the first column.
Thanks! Reviewing now. Jen
I see the problem - metadata assignments for BED datatypes is problematic. I am writing up a ticket to address this (and will share your history as a test example - if not OK - let me know) & trying to come up with a workaround for you to use now. Give me a bit to do all of this - is somewhat complicated.
Thank you. You can use the shared history as a test example.