Question: Subtraction between datasets not showing chromosome number in bed format and is instead showing + signs.
1
gravatar for cmezator
2.1 years ago by
cmezator10
cmezator10 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

ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by cmezator10

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.

Best, Jen, Galaxy team

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson25k

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.

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson25k

Hey Jennifer,

Here is the link to the history I am working on: https://usegalaxy.org/u/carlostorres/h/galaxy-101-2016 Best,

Carlos

ADD REPLYlink written 2.1 years ago by cmezator10

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.

ADD REPLYlink written 2.1 years ago by cmezator10

Thanks! Reviewing now. Jen

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson25k

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.

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson25k

Thank you. You can use the shared history as a test example.

ADD REPLYlink written 2.1 years ago by cmezator10
0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The problem was one that was reported earlier and is still present in the latest release (v 16.07). I have updated the existing ticket with your example and asked the development team to review this as a priority.

Workaround: Upload the data again (downloading the existing datasets first as needed) being sure to assign the datatype in the Upload tool (do not use "autodetect"), removing unnecessary columns first with the tool Cut. This results in just the three correct column assignments and will permit proper usage of the target tool(s).

Please follow the ticket for updates: https://github.com/galaxyproject/galaxy/issues/2175

Thanks for reporting the problem and sharing your example history! Hopefully this will be corrected near-term.

Jen, Galaxy team

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Jennifer Hillman Jackson25k
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