Question: Customising bedtools shuffle command
0
gravatar for kdc15
3 months ago by
kdc1530
kdc1530 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 3 months ago by geek_y9.6k • written 3 months ago by kdc1530

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

ADD REPLYlink modified 3 months ago • written 3 months ago by elisheva70
1
gravatar for geek_y
3 months ago by
geek_y9.6k
Barcelona/CRG/London/Imperial
geek_y9.6k 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 3 months ago • written 3 months ago by geek_y9.6k

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 3 months ago by kdc1530
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