Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: using DREME and .broadpeak file
0
gravatar for alirezamomeni707
3.8 years ago by
alirezamomeni707 • 0
alirezamomeni707 • 0 wrote:

I have chip-seq data and used MACS2 to find peaks (genomic regions enriched for methylation). now I want to find the motifs. I found a tool called "DREME". but the input file for that is .fasta format and what I have is .broadpeak file. do you know how to use DREME and .broadpeak file?
chip-seq • 832 views
ADD COMMENT • link •
modified 3.8 years ago by YaGalbi • 1.5k • written 3.8 years ago by alirezamomeni707 • 0

What kind of Chip-Seq data it is ?

ADD REPLY • link written 3.8 years ago by geek_y ♦ 11k
0
gravatar for YaGalbi
3.8 years ago by
YaGalbi • 1.5k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi • 1.5k wrote:

Have you read the tutorial?

"DREME works best with lots of short (~100bp) sequences. If you have a couple of long sequences then it might be beneficial to split them into many smaller (~100bp) sequences. With ChIP-seq data we recommend using 100bp regions around the peaks."

Have you looked at what is inside the broadpeak file? - it contains positions, you may need to create a fasta file for the positions
ADD COMMENT • link written 3.8 years ago by YaGalbi • 1.5k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1790 users visited in the last hour
_