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
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 -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
29 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment