DC-TAP-seq paper: large input files for figure reproduction

Large input files for the figure-generation workflow of the DC-TAP-seq paper (A systematic survey of distal element-gene regulatory interactions with Direct-Capture Targeted Perturb-seq), code at github.com/EngreitzLab/DC_TAP_Paper. To use them, run bash workflow/scripts/download_large_inputs_from_zenodo.sh from the repository root, then pixi run main-figures. The script downloads every file, places it at its repository path and checks the MD5 sums. Each file can also be downloaded on its own: file_manifest.tsv gives its repository path and how to unpack it (.tar files extract from the repository root; .tsv.gz files are gzipped copies), and file_checksums.md5 lists the MD5 sum of every unpacked file. File Contents compare_replicates_K562_DC_TAP_Seq_1.tar SCEPTRE analysis of K562 DC-TAP-seq replicate 1 alone (SCEPTRE object, gRNA assignments, QC plots). Input to rule make_replicates_plots (replicate concordance). compare_replicates_K562_DC_TAP_Seq_2.tar SCEPTRE analysis of K562 DC-TAP-seq replicate 2 alone. Input to rule make_replicates_plots. compare_replicates_WTC11_DC_TAP_Seq_1.tar SCEPTRE analysis of WTC11 DC-TAP-seq replicate 1 alone. Input to rule make_replicates_plots (Fig. 2d). compare_replicates_WTC11_DC_TAP_Seq_2.tar SCEPTRE analysis of WTC11 DC-TAP-seq replicate 2 alone. Input to rule make_replicates_plots (Fig. 2d). WTC11_DC_TAP_Seq_metadata.rds Per-cell metadata of the WTC11 DC-TAP-seq screen (R data.frame). Input to the WTC11 SCEPTRE input rules (Fig. 2h). WTC11_DC_TAP_Seq_raw_counts_dge.rds Raw gene-by-cell UMI count matrix of the WTC11 DC-TAP-seq screen (R sparse matrix). Input to the WTC11 SCEPTRE input rules (Fig. 2h). WTC11_DC_TAP_Seq_raw_counts_perturb_status.rds gRNA-by-cell perturbation status of the WTC11 DC-TAP-seq screen (R sparse matrix). Input to the WTC11 SCEPTRE input rules (Fig. 2h). results_with_element_gene_pair_categories.tsv.gz DC-TAP-seq results combined with reprocessed Gasperini et al. 2019 results, with element-gene pair categories. Input to rules find_duplicate_pairs (Fig. 2f) and power_to_detect_change_for_all_datasets (Fig. 3b). results_with_element_gene_pair_categories_wo_pos_controls.tsv.gz As above, with the final calls (FDR 20%, positive controls excluded). Input to the Fig. 3a,b and Fig. 5 rules. Following files are required to reproduce the direct versus indirect effects analyses shown in Figure 4 and Extended Data Figures 7, 15 and 16. These are downloaded by code for the respective analyses. File Contents direct_vs_indirect_effects_files.tar.gz Input files from external CRISPR datasets required to compute direct versus indirect effects probabilities by the snakemake workflow in `direct_vs_indirect_effects/compute_direct_vs_indirect_effects`. Downloaded automatically when executing this workflow. ENCODE_Gasperini2019_0.13gStd_MAST_perCRE_GRCh38.tsv.gz Gasperini et al., 2019 data re-analyzed in Gschwind et al., 2026 in ENCODE CRISPR data format. Required analyses shown in Extended Data Fig. 16. Originally produced by: https://github.com/argschwind/ENCODE_CRISPR_data. Gasperini2019_output_MAST_perCRE.tsv.gz MAST cis effects differential expression results for Gasperini et al., 2019 data re-analyzed in Gschwind et al., 2026. Required analyses shown in Extended Data Fig. 16. Originally produced by: https://github.com/argschwind/ENCODE_CRISPR_data. Gasperini2019_output_trans_effects_MAST_perCRE.tsv.gz MAST trans effects differential expression results for Gasperini et al., 2019 data re-analyzed in Gschwind et al., 2026. Required analyses shown in Extended Data Fig. 16. Originally produced by: https://github.com/argschwind/ENCODE_CRISPR_data.