generate a matrix of gene expressions and TFs from bed files

Question

[el24]

Hi everyone, I'm getting familiar with bedtools, and I have a question. How can I generate .bed files for each cell from ATAC-seq data? Imagine, this .tsv data as an example. Thanks!

p.n: This is a similar question but I couldn't find the answer.

[Kevin Blighe]

Please help us to understand better the problem. What data do you currently have, and what data would you ultimately like to produce?

[el24]

Sorry for the confusion, I updated the question :)

[Kevin Blighe]

BED formart is just:

CHR  <TAB>  START  <TAB>  END

So, you can probably generate it via cut

[Ankit]

Give your sample bed files to featurecounts (Subread) . It will provide you matrix.

Or

bedtools coverage can give you number of reads underlying your feature of interest eg. Genes. If your features are same for all samples, then combine the samples parallely to get a matrix