Question: Intersect tool in Galaxy
gravatar for katherinedixon4
3.7 years ago by
katherinedixon410 wrote:

Hi there,

I am using the Intersect tool in Galaxy to find overlapping intervals of peak calls from ChIP-seq data. I haven't been able to determine what the values in the fifth column in the output interval file represent, and was hoping you could help? The values generally range from about 50-1000. Thank you!

galaxy chip-seq • 1.1k views
ADD COMMENTlink modified 3.7 years ago by Jennifer Hillman Jackson24k • written 3.7 years ago by katherinedixon410
gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson24k wrote:


Interval files can vary in the arrangement of columns - this is how they differ from other structured formats such as BED. But in general, if the column order is "BED-like", then this is the score column. How to interpret these depend on the tool used to generate the data. I'd review the manual for the tool to see what the ranges represent. If you click on the pencil icon for the dataset, you'll also maybe see that the 5th column is assigned as "score", or you can assign it yourself, to have it interpreted by the tools that use it (for example, in visualization, such as Trackster). 

Take care, Jen, Galaxy team

ADD COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson24k

Hi Jen,

Thank you for your detailed answer! I have also been trying the new MACS2 on the Galaxy testing site, particularly to use the bdgbroadcall function that is available there. However I'm not sure what the last few columns in the output file represent, and haven't been able to find information about them. I was wondering if you might know what these values are? The file looks like this:

chr1 4999196 5006411 macs2_bdgbroadcall.bdg_broadRegion654 0 . 5005546 5005711 0 1 165 6350 0 0 0
chr1 6740397 6741770 macs2_bdgbroadcall.bdg_broadRegion1178 0 . 6741607 6741762 0 1 155 1210 0 0 0

 Thank you!

ADD REPLYlink written 3.7 years ago by katherinedixon410

Glad that helped! And next time, please ask a new question as a new post, to help us stay organized.

First, I should state that this wrapper is still under development, and on the Test instance, so I wouldn't expect all to be necessarily perfect (due to the wrapper/tool itself but especially configuration of the instance which is under constant revision).

The output file is called:

This is the MACS2 documentation where outputs are defined:

Best, Jen, Galaxy team


ADD REPLYlink written 3.7 years ago by Jennifer Hillman Jackson24k

Thanks Jen!

ADD REPLYlink written 3.6 years ago by katherinedixon410
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