snubar_atac_scripts

This repository saves the scripts used in the manuscript.

Kaile Wang*, Zhenna Xiao*, Yun Yan*, Rui Ye, Min Hu, Shanshan Bai, Emi Sei, Yawei Qiao, Hui Chen, Bora Lim, Steven H Lin, Nicholas E Navin^. Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility. Mol Cell . 2021 Oct 21;81(20):4319-4332.e10. doi: 10.1016/j.molcel.2021.09.026.

SNuBar reads demultiplexing and conversion

As described in the 'Data pre-processing' part in the Methods section, the following 3 scripts were used to pre-process the sequencing reads of SNuBar for spatial/sample barcoding.

1. Snubar-ATAC-fq-convert.pl: Script to transform ATAC cells barcode.
2. Snubar-ATAC-script.sh: Script to process the SNuBar-ATAC data.
3. Snubar-ARC-script.sh: Script to process the SNuBar-ARC data.

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Prepare SNP for Demuxlet

See the pipeline here.