Hello everyone,
I'm currently working with single-cell DamID datasets, focusing on studying protein-DNA interactions. In my dataset for each cell, I have aligned BAM files, counts files in HDF5 format, and count files binned at 100kb intervals. These count files contain the number of unique counts observed for each chromosome and each strand.
Now, I am looking to visualize these binned counts for each cell and also generate a combined average profile. I'm a bit uncertain about how to handle the binned counts using Deeptools to obtain BigWig or BED files for visualizing the enrichment profiles. I have a basic understanding of different file types, but I need guidance on how to proceed with the binned counts.
Any assistance or advice on this matter would be greatly appreciated.
Can you show some top lines of your count files and dimensions of matrix?
Also what exactly you want to plot with Deeptools? Is it enrichment heatmap plot, average plot?
The binned counts look like this:
The dimensions of the matrix are different for each chromosome, here it is 1951 X 1. I want to first plot an average enrichment plot, for instance for chromosome 1, the observed average counts which can be visualised
What does 1,2,3,4,5.... represents. Are these IDs of 100kb intervals? If you can create bedgraph, basically chr-start-end-counts from here then you can convert it to bigwig which can be an input to Deeptools computematrix.