Question: Unable to see my data in the job column
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waliamannu • 0 wrote:
I have registered myself first in the begining. I uploaded two txt files to be analysed.
But when i begin for a job , I am unable to see my data sets in the job column.
The data is succesfully uploaded but dont apear in the job column.
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modified 3.8 years ago
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Martin Čech ♦♦ 4.9k
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4.6 years ago by
waliamannu • 0
With job column you mean the history panel on the right side of your Galaxy workbench? How do you know its successfully uploaded? Usually you see a yellow box in the history panel with a spinning wheel, that box will turn green if the dataset is uploaded.
Dear Bjoern,
The data has been uploaded succesfully as indicated by the green colour. However now if I plan to say join two data sets. the data sets doesnt show up in the tool pull down menu. You need to assign the data for the job right? I do not see any data in there.
Dear Jen,
Thanks for the prompt reply. I understand your queries. satifying everything above I still do not see my data sets in input for a tool in the pull-down menu.
Thanks
Mannu
Hi Mannu, Are you on usegalaxy.org? Also, what tool are you using ("Join two Datasets")? This accepts most tabular datatypes, but what are your inputs set as? Sounds like we are close to a solution. -Jen
Dear Jen,
I am on https://usegalaxy.org/. In the tools section I am trying to perform Operate on Genomic Intervals. I have two seperate gene lists as excel files which I have converted to tab delimited format and I want to find an overlap between the two. For this I am using join or the intesect function from the tools.
Do you mean I have to make my file format into tabular format?
many thanks for helping me out with this.
best regards
Mannu
Mannu - Lucky guess on Excel :)
Yes, tabular is good for many things, but since you are using the Operate on Genomic Intervals tools (not just Text Manipulation Tools) I would go ahead and assign the datatype as "interval". This is still tabular data, but has specific fields assigned. See the wiki below for the details. And if your start coordinate is not already 0-based, use the tool "Compute" to subtract "1" from your start, then the tool "Cut" to rearrange your data (substituting in the new 0-based start, and dropping the old one). Use the tool panel search to find tools by name.
OK - here's the datatype wiki: https://wiki.galaxyproject.org/Learn/Datatypes#Interval
The first two plus the fourth protocols in the "Using Galaxy" paper might be of interest, too. The first demonstrates a join operation, the second how to convert almost any file to interval (as long as the data is in there, it can be arranged and labeled), and the fourth covers all of the Genomic Interval functions. It can be found here: https://usegalaxy.org/u/galaxyproject/p/using-galaxy-2012
Good luck! jen