generate a matrix of gene expressions and TFs from bed files

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4.7 years ago

el24 ▴ 40

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.

ATAC_seq Bedtools • 1.2k views

ADD COMMENT • link updated 4.6 years ago by Biostar 20 • written 4.7 years ago by el24 ▴ 40

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

ADD REPLY • link 4.7 years ago by Kevin Blighe 88k

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Sorry for the confusion, I updated the question :)

ADD REPLY • link 4.7 years ago by el24 ▴ 40

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BED formart is just:

CHR  <TAB>  START  <TAB>  END

So, you can probably generate it via cut

ADD REPLY • link 4.7 years ago by Kevin Blighe 88k

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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

ADD REPLY • link 4.7 years ago by Ankit ▴ 500

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