Entering edit mode
3.5 years ago
dk0319
▴
70
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
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.
This approach worked
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.
You can use the BDGDIFF function of MacS2 to do this.
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.
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.