Question: using DREME and .broadpeak file
0
gravatar for alirezamomeni707
3.8 years ago by
alirezamomeni7070 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 COMMENTlink modified 3.8 years ago by YaGalbi1.5k • written 3.8 years ago by alirezamomeni7070

What kind of Chip-Seq data it is ?

ADD REPLYlink written 3.8 years ago by geek_y11k
0
gravatar for YaGalbi
3.8 years ago by
YaGalbi1.5k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.5k 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 COMMENTlink written 3.8 years ago by YaGalbi1.5k
Please log in to add an answer.

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
_