generate a matrix of gene expressions and TFs from bed files
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.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Reading files from different types as H5AD
written by AlexStar •
-
Questions about supplementary file contents of a GEO dataset
written by Josh •
-
GeneActivity without Fragments file in Seurat for Integrating scRNA-seq and scATAC-seq
written by el24 •
-
Where do I share a single-cell dataset?
written by Lluís R.
-
Non-zero chrY CpG sites in female samples
written by lotus28
-
Error when reading microarray idat files from illumina
written by salamandra
-
Multiplatform batch correction using combat
written by Devyani •
-
NCBI GEO/GSM/SRA conventions: Is raw data a part of the SRA or a supplementary file?
written by abe •
-
Methylation levels at specific sites
written by firatuyulur
-
Peak Calling with MACS (treat and control samples)
written by ukpersia1 •
Please help us to understand better the problem. What data do you currently have, and what data would you ultimately like to produce?
Sorry for the confusion, I updated the question :)
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
BED formart is just:
So, you can probably generate it via
cut