Customising bedtools shuffle command

Question

[kdc15]

Hi, I am trying to use the bedtools shuffle command to shuffle transcription factor binding locations. However, I was wondering if the "genome" option could be interchangeable with my own customised file of enhancers? Is it possible to have a file like this in the same format?

[elisheva]

Could you please upload some lines of your file? So it will be easier to understand what exactly do you want.

Answer 1

[GouthamAtla]

If you have read the manual, you could do that with -incl -excl options.

If I understand your question correctly, your enhancer bed file should be given as -incl, so the random regions matching your TF bed file will be generated from enhancers.

[kdc15]

for my -incl option I have selected the mappable regions (with a CRG score of 1) of the genome. Is it better to replace this with my enhancer file?