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Question: Change Tracking Id to Gene name
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gravatar for VY
22 months ago by
VY • 120
London
VY • 120 wrote:

Hello,

I'm not sure if this is something that can be done in galaxy, but if anyone knows how to do it in R that would help aswell.

I've run cuffdiff on my samples and I've selected the output count file function.

When I look at my cuffdiff gene count tracking file, all the rows are under the tracking id (XLOC_00001 etc). Looking at my gene differential expression file though, I can see both the tracking id and the gene name (BRCA1 etc) as I had used a reflat gtf.

I'd like to use the normalised counts file for some other stuff but having the tracking id displayed is not helpful, and changing it manually into the gene names would be too time consuming and daunting. Does anyone know how I can match the tracking id in the one file to the gene name in the other? Either or galaxy or in R?

Any suggestions would be really helpful.

Thanks V
rna-seq rnaseq cuffdiff • 810 views
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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by VY • 120
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gravatar for Jennifer Hillman Jackson
22 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Datasets can be joined on a common identifier and the merged dataset columns cut (reduced/reordered) to produce the desired final result dataset.

  • To join any two datasets based on common tracking ids, use the tool Join, Subtract and Group > Join two Datasets side by side on a specified field
  • To cut out columns from a dataset and output in any order, use the tool Text Manipulation > Cut columns from a table
  • After using the tool Cut, click on the pencil icon to reset the datatype (first, and save) and column assignments (second, and save), if the cut action produces something other than a generalized tabular file and you want something more specific. Example: Cut was used to produce bed, interval, etc. that meets one of those datatype's specifications, and that datatype format is required by downstream tools.

The Galaxy 101 goes through a simple walk-through of data manipulation tools that are similar and might be useful to learn more about how to use text manipulation and related tools. If a tool you want to use is not in the tutorial, usage can be found on the tool form (many are similar to line-command utilities - there is no need to do this manually or by hand): http://usegalaxy.org/galaxy101

Hopefully this helps! Jen, Galaxy team
ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k
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