├── .gitignore ├── README.md ├── Snakefile ├── cluster.json ├── compare_to_10x ├── 10x_NextGEM │ ├── index.txt │ └── outs │ │ └── sample_info.csv ├── 10x_NextGEM_20210115_seurat_v2.nb.html ├── 10x_v1 │ ├── index.txt │ └── outs │ │ └── sample_info.csv ├── 10x_v1_20210115_seurat_v2.nb.html ├── README.md ├── plate_downsample │ └── outs │ │ └── sample_info.csv └── plate_ds_20210118_seurat.nb.html ├── config.json ├── old_obsolete ├── ATAC_seq_read_length_curve_fitting.ipynb ├── README.md ├── Snakefile_basespace ├── Snakefile_ena ├── Th2_time_series_ATACseq_2d_PCA.ipynb ├── cluster.json ├── frag_distr.py └── run.sh ├── scripts ├── collect_metadata.py ├── generate_count_csc_mtx.py ├── generate_fragments_file.sh ├── get_depth_mr.sh ├── get_dup_level.sh ├── get_frac_open.sh ├── get_frip.sh ├── get_lib_size.sh ├── get_ufrags_mt.sh └── list_bam.sh └── submit_snake.sh /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | .ipynb_checkpoints/ 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