Question: ATAC seq specific region extraction
0
gravatar for krushnach80
19 months ago by
krushnach80470
krushnach80470 wrote:

I have set of induced vs induced atac seq data , i did try to plot the tss region with deeptools i was able to do but i want to extract specific promoter regions .How can i do that what tools do i use to do the same ?I want to see at particlular promoter site how the chromosome region is ,is it open or close .

Any suggestion or help would be highly appreciated

chip-seq • 634 views
ADD COMMENTlink modified 19 months ago by Devon Ryan88k • written 19 months ago by krushnach80470
2
gravatar for Devon Ryan
19 months ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

It's difficult to parse what you really want, but I would presume you should just load the BAM/bigWig files in IGV and look at those regions. If you want instead to plot specific regions with deepTools then use only those as input into computeMatrix (you can alternatively use computeMatrixOperations to filter things).

ADD COMMENTlink written 19 months ago by Devon Ryan88k

I have done that I mean see those region in IGV

If you want instead to plot specific regions with deepTools then use only those as input into computeMatrix

cani I do that for specific regions ? I mean lets say I want to see what is happening with chr 7 and can I plot the same with the computeMatrix function?

ADD REPLYlink modified 19 months ago by Devon Ryan88k • written 19 months ago by krushnach80470
1

You can either run computeMatrix with a specific set of regions or with all regions and then filter the output with computeMatrixOperations. There's no filtering in the plot* functions. computeMatrix doesn't plot anything, it just makes a matrix of values for plotting.

ADD REPLYlink written 19 months ago by Devon Ryan88k
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