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
I have done that I mean see those region in IGV
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?
You can either run
computeMatrix
with a specific set of regions or with all regions and then filter the output withcomputeMatrixOperations
. There's no filtering in the plot* functions.computeMatrix
doesn't plot anything, it just makes a matrix of values for plotting.