FAQs

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

There are two options:

1. 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

2. 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.

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.

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