├── .gitignore ├── LICENSE ├── README.md ├── config ├── README.md ├── config.yaml └── samples.tsv ├── gke └── config.yaml ├── legacy ├── envs │ ├── align_bowtie2.yaml │ ├── bam_to_frag.yaml │ ├── barcode_corr.yaml │ ├── barcode_corr_old.yaml │ ├── dedup_bam.yaml │ ├── frac_mito.yaml │ ├── frag_tar.yaml │ ├── matcha.yaml │ ├── strip_fastq.yaml │ └── trim_adapter.yaml ├── legacy_configs.yaml ├── old.smk ├── samples.tsv ├── scripts │ ├── align.sh │ ├── bam_to_frag.sh │ ├── dedup_bam_pe.sh │ ├── filter_multiplets.py │ ├── frac_mito.py │ ├── pbc_stats.awk │ ├── process_10x_barcodes.py │ ├── process_10x_barcodes_matcha.py │ ├── process_ren_barcodes_matcha.py │ └── summarize_fragment_stats.py └── test_data │ ├── .gitignore │ ├── assign_multimappers_v1.5.py │ ├── bam_to_fragments.py │ ├── barcode_matching_test.snakemake │ ├── config.yaml │ ├── ren_lab │ ├── ren_barcodes_T7.tsv │ └── ren_barcodes_i5.tsv │ ├── simple_pipeline.snakemake │ └── summarize_fragment_stats.py ├── utils ├── check_config.py ├── plot_qc.py └── plot_qc_bulk.py └── workflow ├── Snakefile ├── envs ├── analyses.yaml ├── fastqs.yaml ├── filtering.yaml ├── fragments.yaml ├── mapping.yaml └── portal.yaml ├── rules ├── analyses.smk ├── fastqs.smk ├── filtering.smk ├── fragments.smk ├── mapping.smk ├── metadata.smk └── submit.smk └── scripts ├── assign_multimappers.py ├── bam_to_fragments.py ├── barcode_revcomp_detect.py ├── build_archr_project.R ├── build_bulk_caper_config.py ├── collate_metadata.py ├── detect_multiplets.py ├── encode_query.py ├── encode_resubmit.py ├── encode_submit.py ├── filter_mito.py ├── match_barcodes.py ├── parse_archr_qc.R ├── pbc_stats.py ├── write_file_metadata.py └── write_qc_metadata.py /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | .snakemake -------------------------------------------------------------------------------- /LICENSE: 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