Question: generate a matrix of gene expressions and TFs from bed files
0
gravatar for el24
4 months ago by
el2410
USA
el2410 wrote:

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 • 183 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 4 months ago by el2410

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

ADD REPLYlink written 4 months ago by Kevin Blighe63k

Sorry for the confusion, I updated the question :)

ADD REPLYlink written 4 months ago by el2410
1

BED formart is just:

CHR  <TAB>  START  <TAB>  END

So, you can probably generate it via cut

ADD REPLYlink written 4 months ago by Kevin Blighe63k

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 REPLYlink written 4 months ago by Ankit140
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