ATAC seq specific region extraction

Question

[1769mkc]

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

Answer 1

[Devon Ryan]

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).

[1769mkc]

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?

[Devon Ryan]

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.