scATAC-seq (Graybuck 2021) Pipeline

This single cell ATAC-seq pipeline includes a set of tools necessary for pre-processing ATAC-Seq libraries prepared as in (Graybuck et. al 2021).

This pipeline adapted from following study: Paper, Code and Data

Steps:

1. Trim Galore tool is used to remove adapters from reads.
2. Trimmed and untrimmed reads are aligned to the reference using Bowtie
3. Duplicates reads are deleted using Samtools.
4. MACS2 is used for calling peaks within ATAC-Seq reads.
5. ChipSeeker package (R) is incorporated to annotate peaks.

Program Versions:

• Star v2.5.3
• Samtools v1.3
• Bowtie v1.1.1
• Bedtools v2.29.2
• Igvtools v2.5.3
• r-base v4.0.0
• Ucsc-wigToBigWig v377
• Macs2 v2.2.7
• Homer v4.11.0
• Trim-galore v0.6.2

Pipeline Container:

• Docker: dolphinnext/graybuck2021_scatacseq_pipeline:latest
• GitHub: dolphinnext/graybuck2021_scatacseq_pipeline