Hi I am trying to do peak-calling using MACS for some of my H3K4me3 ChIP-seq data. Using the default p-value of 1e-5 I only obtained 500+ peaks. But if I change the p-value to 1e-4 I got 1500+ peaks and by increasing it more to 1e-3 I got 7000+ peaks! My question is how do I know which is the best p-value to use? I would like to get more peaks but I also don't want any false positive peaks. Thanks for your help!
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
There is no best number and it completely depends on your data set. Load the data onto a genome visualizer and look at the peaks it is calling. Use your best judgement and validate by qPCR. Fold enrichment is another important and easy to understand parameter to consider.--------------
Ethan
Comment
-
dgrayson, if you use the -w option when running MACS you will generate a wig file which can be uploaded and visualized on a genome browser. I like to use the -w option with the -S option so that I only generate a single wig file instead of one for each chromosome.
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, 04-11-2024, 12:08 PM
|
0 responses
59 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
57 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
51 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
55 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment