Question: Customising bedtools shuffle command
0
gravatar for kdc15
14 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 14 months ago by geek_y10k • written 14 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 13 months ago • written 14 months ago by elisheva100
1
gravatar for geek_y
14 months ago by
geek_y10k
Barcelona
geek_y10k 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 14 months ago • written 14 months ago by geek_y10k

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 14 months ago by kdc1530
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1220 users visited in the last hour