Question: select a specific hits from XML output
0
gravatar for najoua.mghazli
4 weeks ago by
najoua.mghazli0 wrote:

Hello, I've generated an XML output from a megablast using tblastn on Galaxy, and now I want to select from this output the sequences that respond to my criteria (such as identity percentage, long coverage, short coverage ...). I checked Parse blast XML output tool but it doesn't take any specified parameter, does anyone have an idea on how can I select a specific hits from my sequences ? Thank you,

Best.

blast xml tabular galaxy • 78 views
ADD COMMENTlink modified 24 days ago • written 4 weeks ago by najoua.mghazli0
1
gravatar for Jennifer Hillman Jackson
27 days ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi,

The tool Parse blast XML is where to start. This doesn't take any additional parameters - it only parses out the original results into a tabular format where it can be further queried.

The help at the bottom of the form explains how to generate the percent identify. The query/target lengths and the alignment lengths can be used to compute coverages using the same tool (Compute). From there you can filter on those values using other tools in the Text Manipulation, Filter and Sort, and Join, Subtract and Group tool groups, for example Filter data on any column using simple expressions. You can graph the data using the charts under Visualize (top masthead, or the small graph icon within a tabular dataset).

Thanks! Jen, Galaxy team

ADD COMMENTlink written 27 days ago by Jennifer Hillman Jackson25k
0
gravatar for najoua.mghazli
24 days ago by
najoua.mghazli0 wrote:

Thanks a lot for your reply,it was helpful.

ADD COMMENTlink written 24 days ago by najoua.mghazli0
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