Ziliang Luo
This is a pipeline for analyzing single cell ATACseq data.
It takes the mapping bam files (e.g. from Cellranger), filters the low quality reads by SAMtools, removes PCR duplicates by Picard, modifies the CB barcode, and makes Tn5 insertion bed files.
Make sure the these software (samtools, picard, bedtools, and macs2) are installed/loaded in the PATH. Python module pysam is also required.
module load SAMtools
module load picard
module load BEDTools
module load MACS2
This step calls FixingBarcodeName.py and makeTn5bed.py for the ananlysis, make sure their path is correct.
usage: bam2bed_scatac_8.23.23.py [-h] -b <bam> -s <sample_name> -o <output_dir> [-x <cpu#>] -r <ref_index> [-l <black_list>]
This script processes raw mapping bam file (e.g. from Cellranger), and make Tn5 insertion bed file.
options:
-h, --help show this help message and exit
-b <bam>, --bam <bam> the input bam file
-s <sample_name>, --sample <sample_name> the sanmple name
-o <output_dir>, --out <output_dir> the output directory
-x <cpu#>, --cpu <cpu#> the number of cores used
-r <ref_index>, --ref <ref_index> the genome reference index. Use samtools faidx to build the index
-l <black_list>, --bklst <black_list> a bed file black list that contains the low-complexity and homopolymeric regions, organelle sequence regions, Tn5 cutting bias regions and potential collapsed regions in the reference genome. (see methods in [Marand et al., 2021](https://doi.org/10.1016/j.cell.2021.04.014))
python bed2bw_scatac_8.23.23.py <script_dir> <ref_idx> <bedGraphToBigWig_dir> <sample_name>