FAQs

How to proceed from 10x cellranger-atac output bam file?

We provided a module convert10xbam, which convert 10x cellranger-atac style position sorted bam file to scATAC-pro style bam file.

scATAC-pro -s convert10xbam -i 10x_positionsort.bam -c configure_user.txt -o output

It will output bam file of scATAC-pro style in output/mapping_result/, and mapping qc stats and fragment.bed file in output/summary/. Users can then use all the other modules in scATAC-pro.

How to merge different peaks called from differnt samples or conditions?

We provided a module mergePeaks, which take peaks files and a distance paramter separated by comma as input.

scATAC-pro -s mergePeaks -i peakFile1,peakFile2,peakFileN,200 -c configure_user.txt -o output

It will sort peaks and merge those with gap less than 200bp, and merged peaks will be saved under output/peaks/merged_peaks.bed

How to reconstruct peak-by-cell matrix after updating the peak file?

We proveided a module reconstMtx, which takes a peak file, a framents.txt file and a barcodes.txt file separated by comma as input:

scATAC-pro -s reconstMtx -i peakFile,fragmentFile,barcodesFile -c configure_user.txt -o output

The reconstructed matrix will be saved under reConstruct_matrix/ under the same path as the barcodesFile.