Question: Using bedtools to identify genes that have overlapping chip-seq peaks
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gravatar for dk0319
6 weeks ago by
dk03190
dk03190 wrote:

I was interested to know if bedtools can be used to retrieve gene names from multiple files that have shared peaks overlap. I am new to bedtools and I just wanted to confirm that this is indeed possible and if anyone can recommend any resources in addition to the manual. Cheers

chip-seq bedtools • 199 views
ADD COMMENTlink modified 6 weeks ago by Biological information research group of Harbin medical university daqing campus10 • written 6 weeks ago by dk03190
1

If you provide a bedtools-compatible file (BED, GTF) that contains the gene names then yes. For more details one would need details on your files.

ADD REPLYlink written 6 weeks ago by ATpoint42k
1

You can use the bedtools intersect function to find those peaks that overlap between multiple bed files. You can then use the closest function in bedtools to annotate the nearest gene to those peaks.

ADD REPLYlink written 6 weeks ago by emilyprice1620

You can use the BDGDIFF function of MacS2 to do this.

ADD REPLYlink modified 6 weeks ago by zx87549.7k • written 6 weeks ago by Biological information research group of Harbin medical university daqing campus10

I have removed maybe useful but irrelevant weblinks for this post. I suggest you add those weblinks to your profile page - Biological information research group of Harbin medical university daqing campus.

ADD REPLYlink written 6 weeks ago by zx87549.7k

Can you elaborate on how this answer related to the question? OP is asking about intersection, you mention a tool for a differential analysis. Edit: Moved this answer to comment as (imho) does not answer the question. Please comment if inappropriate.

ADD REPLYlink modified 19 days ago • written 6 weeks ago by ATpoint42k
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