bio-workflows-atacseq-pipeline

To process ATAC-seq FASTQ files for peak calling and footprinting, run the end-to-end pipeline. It handles QC, alignment, BAM processing, peak calling with MACS3, differential accessibility with DiffBind, and TF footprinting with TOBIAS.

To identify differential accessibility across ATAC-seq conditions, use DiffBind to compare accessible regions across multiple samples. The pipeline quantifies condition-specific regulatory regions and infers TF dynamics.

Transcription factor footprinting with TOBIAS uses aligned ATAC-seq reads and motif resources to infer TF binding dynamics. It processes accessible regions from MACS3 peaks to generate footprinting insights for regulatory analysis.

Yes, you need Bowtie2 and a reference genome with motif resources to run this ATAC-seq pipeline. Additional dependencies include fastp, samtools, bedtools, MACS3, DiffBind, TOBIAS, and deepTools for full end-to-end processing.

Yes, you can use this ATAC-seq workflow for treated and control samples. It supports flexible analyses across multiple samples and conditions, enabling discovery of condition-specific regulatory regions and TF activity differences.

An end-to-end ATAC-seq workflow includes QC steps via fastp, alignment with Bowtie2, BAM processing with samtools and bedtools, peak calling quality metrics, and deepTools QC metrics to ensure reliable accessible region identification.