Supplementary Data for: BAGFOOT2 – differential transcription factor footprinting from ATAC-seq (protocol)

1. Reference Data (Configuration) This dataset contains the genomic background files and nucleotide codes required for the MASA (with HOMER motif enrichment option) software/pipeline. The data covers Human (hg19) and Mouse (mm10) reference genomes. Extract these files into your MASA configuration directory to enable analysis on specific genome builds. hg19_nuccode_v1.0.tar.gz : Nucleotide code mapping files for Human genome (hg19). mm10_nuccode_v1.0.tar.gz: Nucleotide code mapping files for Mouse genome (mm10). hg19_files_v1.0.tar.xz: Motif DB for Human (hg19). mm10_files_v1.0.tar.xz: Motif DB for Mouse (mm10). 2. Vignette & Reproduction Data (Fed vs Fasted) These files allow users to reproduce the analysis presented in the MASA manuscript and vignette. bg_files_fed_fasted.tar.gz : Final Output Directory. Contains the complete MASA results for the Fed vs Fasted comparison, except the nuccode files. bam_merged.tar.gz : Merged BAM files combining replicates for each condition. bam_replicates.tar.gz : Raw alignment files (BAM) for individual replicates (3 Fed, 3 Fasted). (Note: Large file) tag_directories.tar.gz : Intermediate tag directories generated by HOMER during the MASA pipeline execution. macs2.tar.gz : MACS2 peak calling results (narrowPeak files) generated from the merged BAM files for each condition (Fed and Fasted).