Using bedtools to identify genes that have overlapping chip-seq peaks
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
• 2,364 views
•
link
updated
by
Biological information research group of Harbin medical university daqing campus •
•
written
by
dk0319 •
•
written
by
dk0319 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How best to handle multiple probes for single genes in survival analysis of Geo data
written by dk0319 •
-
Database for Enhancers with Coordinates
written by dk0319 •
-
Interpret Bedtools Overlap?
written by kstangline •
-
Selecting genotypes for a specific chromosome belonging to a specific patient from a multi patient …
written by dk0319 •
-
Use BioMart to get gene names for transcripts with isoform ID (e.g. NM_000014.6)
written by dk0319 •
-
Tools for Discovering Genes Containing a DNA motif
written by dk0319 •
-
Whole Genome Seq Analysis Software for Identifying Specific Gene Variants
written by dk0319 •
-
Resources for learning how to submit jobs in unix-based cluster
written by dk0319 •
-
Retrieve sequences from cluster node
written by enxds6 •
-
Remove Intronic Regions in .BAM
written by K.Nijbroek •
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.
I now have a bed file consisting of my target peaks in the following format:
chrI Start Stop
How could I go about assigning the corresponding gene ID's to the peak?
I tried bedtools annotate and all it gave me was the coverage -Cheers
This approach worked
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.
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.