Question: Customising bedtools shuffle command
0
gravatar for kdc15
21 months ago by
kdc1540
kdc1540 wrote:

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?

ADD COMMENTlink modified 21 months ago by geek_y11k • written 21 months ago by kdc1540

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

ADD REPLYlink modified 20 months ago • written 21 months ago by elisheva100
1
gravatar for geek_y
21 months ago by
geek_y11k
Barcelona
geek_y11k wrote:

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.

ADD COMMENTlink modified 21 months ago • written 21 months ago by geek_y11k

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?

ADD REPLYlink written 20 months ago by kdc1540
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