Question: VERY new to Galaxy: How do I query by row and keep rows with specific values
1
gravatar for callan.brownfield
15 months ago by
callan.brownfield10 wrote:

Hi - I've been using Galaxy for about a week now on my own. I'm a total newcomer this world, so pardon if this is a relatively simple question that I am unable to explain well.

I am using Galaxy to analyze data from a HiSeq platform. I have sorted the data in batches down to the calls that I want it to make (no intronic mutations, no synonymous SNVs, etc).

I have kept exonic mutations as well as splice site mutations. The exonic mutations in a specific gene may be associated with 1-8 NM values. I have a list of the canonical NM values that I would like to keep/select for, and the rest I would like to get rid of. So, I am trying to query rows to keep 'splicing' and 'exonic' mutations, but then also only end up with the canonical NM value at the end. For example, a TP53 exonic mutation has 8 NM values associated with it in the same row, and I would like to keep that row, then select for one specific NM value (NM_000546), and get rid of the other values.

Does this make sense? How would I best accomplish this?

Thanks, Callan

ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson25k • written 15 months ago by callan.brownfield10
0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

What is the format of your file? Tabular of some variation?

Use the tools under these tool groups at Galaxy Main (http://usegalaxy.org) with tabular dataset to parse, filter, and rearrange content in a variety of ways:

  • Text Manipulation
  • Datamash
  • Convert Formats
  • Filter and Sort
  • Join, Subtract and Group

If you have a specific operation in mind, searching in the tool panel is one way to quickly find tools that could be appropriate. Most simple unix operations are wrapped. These are also often named similarly as operations one would do in common text editing tools (such as Excell). In short, a combination of tools is probably needed for the data reduction you explain. Once you work out the process, save that into a Workflow for future use, if this is something you might do again. A workflow can be used as a "custom tool" that can be executed with a single click.

If working somewhere else, the tools at Galaxy Main can be reviewed and any not present could be installed into a local/cloud instance that you administer or that you have input on which tools will be installed by the server's administrator.

To understand more about using Galaxy, please see:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson25k
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