What tool does everyone use to annotate ChIP-Seq peaks (i.e. nearest gene, etc). Is there a linux source I could download somewhere for it?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
I suggest either:
a. Galaxy's "Operate on Genomic Intervals": http://main.g2.bx.psu.edu/
or
b. BEDTools (admittedly my own command-line software). You would download genes and whatever annotations you are interested in (BED format) and then use the tools to find closest genes (closestBed), etc.
bedtools.googlecode.com
Aaron
-
Originally posted by quinlana View PostI suggest either:
a. Galaxy's "Operate on Genomic Intervals": http://main.g2.bx.psu.edu/
or
b. BEDTools (admittedly my own command-line software). You would download genes and whatever annotations you are interested in (BED format) and then use the tools to find closest genes (closestBed), etc.
bedtools.googlecode.com
Aaron
Can BEDtools find insersections in more than 2 bed files? For example, if I am doing ChIP-Seq for Factor A, B, C, & D and I want a single bed file telling me all the places enriched for all of the factors or 3 out of 4 etc.
Comment
-
Originally posted by RockChalkJayhawk View PostAaron,
Can BEDtools find insersections in more than 2 bed files? For example, if I am doing ChIP-Seq for Factor A, B, C, & D and I want a single bed file telling me all the places enriched for all of the factors or 3 out of 4 etc.
BEDTools cannot do what you ask in a single command. However, there are multiple ways to do this with a couple commands. I demonstrate two possible solutions below (assuming I understood you correctly).
Based on your example, let's assume you have four BED files, each representing regions of enrichment for A, B, C, and D, respectively.
The following command will return all of the regions enriched for A that overlap (by at least 1bp) with regions enriched for B,C and D. The "-u" returns a unique entry even when multiple overlaps are found
Code:$ intersectBed -a A.bed -b B.bed -u | \ intersectBed -a stdin -b C.bed -u | \ intersectBed -a stdin -b D.bed -u > ABCD.bed
An alternate and perhaps simpler way is to count the number of overlaps between A/B, A/C, A/D. The example below assumes each BED file has 6 columns (chrom, start, end) and the fourth column (hence the cut -f 4) is the count of overlaps b/w A and B which is returned by the "-c" option.
# Count the overlaps b/w A and the others. Every entry in A will have a count. It will be 0 if there were no overlaps
Code:$ intersectBed -a A.bed -b B.bed -c | cut -f 4 > AtoB.counts $ intersectBed -a A.bed -b C.bed -c | cut -f 4 > AtoC.counts $ intersectBed -a A.bed -b D.bed -c | cut -f 4 > AtoD.counts
Code:$ paste A.bed AtoB.counts AtoC.counts AtoD.counts > AwithCounts.bed
Code:chr1 100 200 0 2 1 chr1 200 300 1 1 2 ... chrY 100 200 0 0 0
The second entry says that this A interval was also enriched in all 3 others.
The third entry says that this A interval was not enriched in any others.
You would repeat for B, C and D and could then write a basic awk or perl script to ask your questions with such an output.
There are other ways to tackle this and obviously subtleties to the questions asked, but I hope this helps you get the ball rolling, as it were.
Aaron
Comment
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 11:49 AM
|
0 responses
15 views
0 likes
|
Last Post
by seqadmin
Yesterday, 11:49 AM
|
||
Started by seqadmin, 04-24-2024, 08:47 AM
|
0 responses
16 views
0 likes
|
Last Post
by seqadmin
04-24-2024, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
61 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
Comment