generate a matrix of gene expressions and TFs from bed files
0
0
Entering edit mode
15 months ago
el24 ▴ 20

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 • 333 views
ADD COMMENT
0
Entering edit mode

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
0
Entering edit mode

Sorry for the confusion, I updated the question :)

ADD REPLY
1
Entering edit mode

BED formart is just:

CHR  <TAB>  START  <TAB>  END

So, you can probably generate it via cut

ADD REPLY
0
Entering edit mode

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

Login before adding your answer.

Traffic: 2396 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6