FAQs

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

• Using reprocess_cellranger_output module (from v1.4.3)

    $ scATAC-pro -s reprocess_cellranger_output
                 -i cellranger_generated.bam_file,cellranger_generated_fragments.tsv.gz_file
                 -c configure_user.txt

• To break it down or using a older version:
  • To get full functions of scATAC-pro, 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.txt file in output/summary/. Users can then use all the other modules in scATAC-pro.

• You can still use part of scATAC-pro modules using 10x cellranger style bam and fragments file. That means if you are not interested in get mapping QC metrics or extracting bam file for each cell subpopulation, you do not have to run convert10xbam module. For example, you can directly use 10x cellranger-atac style bam file to call_peak module and 10x style fragment.tsv file as inputs for get_mtx module.

scATAC-pro -s get_mtx -i YOUR_10x_FRAGMENTS.tsv,Your_Peak_file -o output -c configure_user.txt

• You are able to run other modules such as qc_per_barcode, call_peak, call_cell, clustering, motif_analysis, reConstMtx, and integrate module without running convert10xbam as well.

How to merge different peaks called from different data sets?

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,reconstructedMtxDir(optional) -c configure_user.txt -o output

The reconstructed matrix will be saved by default under reConstruct_matrix/ under the same path as the barcodesFile, if reconstructedMtxDir is not provided.

How to perform downstream analysis in R