Question: gff file of constituent enhancer For Young algorithm
gravatar for dimitrischat
2.4 years ago by
dimitrischat120 wrote:

does anyone know where to find these enhancer gff files ?

gff must have the following columns: 1: chromosome (chr#) 2: unique ID for each constituent enhancer region 4: start of constituent 5: end of constituent 7: strand (+,-,.) 9: unique ID for each constituent enhancer region NOTE: if value for column 2 and 9 differ, value in column 2 will be used

assembly • 1.1k views
ADD COMMENTlink modified 2.3 years ago by Biostar ♦♦ 20 • written 2.4 years ago by dimitrischat120

What is the exact question you want to answer, what input data do you have? The way you ask this question implies that you (no offense meant) do not really know what this tool does.

ADD REPLYlink written 2.4 years ago by ATpoint42k

PURPOSE: To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)

input: files of sequencing reads for factor of interest and control

i downloaded example data files to check out how it "runs" but it only contains hg18 gff file.

hg18 is old thats why i want to find hg19.. also in case our lab need to check mouse data or other organisms i would like to know where i could find these files.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by dimitrischat120

Thanks, I can read the description from ROSE myself, no need to copy/paste this. I was referring to what biological question you want to answer. Anyway, what you need is a predefined list of enhancer regions. As these guys are strongly cell type (and experiment)-specific, you'll have to call them from your data (that is why I was asking what data you have, are they even suitable to call enhancers: is this a transcription factor or a histone mod)? Please elaborate.

ADD REPLYlink written 2.4 years ago by ATpoint42k

H3K27Ac histone mod - Human (RPMI-8402) cells. Do i call them with macs2? I am sorry but obviously i am a newbie

ADD REPLYlink written 2.4 years ago by dimitrischat120

Hi Dimitrischat, As I am also new with this set of analysis and curious to ask, did you figure out the answer to your question? If you don't mind can you please share your experience here with the community?

ADD REPLYlink modified 14 months ago • written 14 months ago by Researcher60
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1825 users visited in the last hour