Question: gff file of constituent enhancer For Young algorithm
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gravatar for dimitrischat
5 months ago by
dimitrischat50
dimitrischat50 wrote:

https://bitbucket.org/young_computation/rose/overview

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 • 233 views
ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 5 months ago by dimitrischat50

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 5 months ago by ATpoint11k

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 5 months ago • written 5 months ago by dimitrischat50

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 5 months ago by ATpoint11k

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 5 months ago by dimitrischat50
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