Question: Help with intersect -BedTools, WindowBed
0
gravatar for kon.klaourakis
2.0 years ago by
kon.klaourakis0 wrote:

Hello,

I have uses WindowBed in order to find the overlapping peaks of two bed files. Although the output is the expected one, some peaks are written multiple times ( image) http://postimg.org/image/oriw1zm07/. Is there a way to eliminate this and only produce the original peaks of file A or B??

Thank you very much for your replies, Konstantinos Klaourakis

ADD COMMENTlink modified 2.0 years ago by Jennifer Hillman Jackson25k • written 2.0 years ago by kon.klaourakis0
3
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The tool Text Manipulation > Unique occurrences of each record will perform a "sort -u" on the existing data. There is no provenance about which original input file donated each row. However, the tool Join, Subtract and Group > Compare two Datasets to find common or distinct rows could be used after to divide the result into two files (compare against the original files). From there you could Add column to an existing dataset for each then merge it all back together again with Concatenate.

There are other possibilities to sort or group the data (replace above or do additional manipulations after sorting uniquely). See these tool groups for options:

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

Hopefully this helps, Jen, Galaxy team

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Jennifer Hillman Jackson25k

You are the real MVP, thank you very much for your help!!

ADD REPLYlink written 2.0 years ago by kon.klaourakis0

Thank you! If you have time, please accept the answer (if/when it works out, it did with my small test dataset) so that others on this site can easily find the solution should they need to do the same manipulations. Do this by hovering over the left side of the reply and clicking on the checkmark.

ADD REPLYlink written 2.0 years ago by Jennifer Hillman Jackson25k
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