can it be applied to a single BAM file (scATAC-seq) and a single 10X scRNA-seq data?

[x811zou]

Hi!
I have a sample (no labeling) of stem cell differentiation data in both scRNA-seq and scATAC-seq, but I only have one BAM file from 10x. Just wanna make sure that your method could be applied to my data, coz I want to get combined clustering result.
Thank you for your help!

[timydaley]

Hi Xue,
Our R package scABC has the ability to read in and obtain count matrix files from a single bam ATAC-seq file, using the read group tag. The package is available at https://github.com/SUwonglab/scABC. The following commands should get you the counts file.

devtools::install_github("SUwonglab/scABC")
bamfile = "input.bam"
peakfile = "peaks.bed"
peaks = selectPeaks(peakfile)
counts = scABC:: getCountsMatrix(bamfile, peaks, byReadGroup = TRUE, RGtag = 'CB') # Or whatever your read group tag is
write.table(as.matrix(counts), file = "counts.txt", sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)

@durenzn Should the cell names be written to the file? If so, then set col.names = TRUE

This should then be suitable for input for CoupledNMF. Let us know. We haven't done this before.