Help with intersect -BedTools, WindowBed

Question: Help with intersect -BedTools, WindowBed

2.5 years ago by

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 ( ) 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

usegalaxy windowbed intertsect bedtools chip-seq • 806 views

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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by kon.klaourakis • 0

2.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 2.5 years ago • written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 2.5 years ago by kon.klaourakis • 0

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 REPLY • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k

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