rules 
tools
rocketchip
.snakemake/
*/.snakemake/
*/.ipynb_checkpoints
chip_seq/peak_counts/
chip_seq/*heatmap.pdf
chip_seq/new_peak_counts.csv
chip_seq/old_peak_counts/
chip_seq/single/
chip_seq/snakefiles.yaml
chip_seq/subsetted_data/
functional_test/project_files/
functional_test/snakefiles/
functional_test/seq_data/
exp_vs_obs/seq_data/paired_narrow/
exp_vs_obs/seq_data/paired_broad/
exp_vs_obs/seq_data/single_narrow/
exp_vs_obs/seq_data/single_broad/
exp_vs_obs/seq_data/archive/
exp_vs_obs/seq_data/__pycache__/
exp_vs_obs/project_files/
exp_vs_obs/snakefiles/
exp_vs_obs/.ipynb_checkpoints/
exp_vs_obs/seq_data/seqdata/
exp_vs_obs/seq_data/seqdata.tar.gz
run_times/yeast/00_logs/
run_times/yeast/01_raw_data/
run_times/yeast/02_fastqc_analysis/
run_times/yeast/03_sam_files/
run_times/yeast/04_bam_files/
run_times/yeast/05_bigwig_files/
run_times/yeast/06_macs3_peaks/
run_times/yeast/sacCer3/
run_times/yeast/paired/
run_times/worm/00_logs/
run_times/worm/01_raw_data/
run_times/worm/02_fastqc_analysis/
run_times/worm/03_sam_files/
run_times/worm/04_bam_files/
run_times/worm/05_bigwig_files/
run_times/worm/06_macs3_peaks/
run_times/worm/ce11/
run_times/worm/paired/
run_times/fruitfly/00_logs/
run_times/fruitfly/paired/
run_times/human/00_logs/
run_times/human/paired/
run_times/human/01_raw_data/
run_times/human/02_fastqc_analysis/
run_times/human/03_sam_files/
run_times/human/04_bam_files/
run_times/human/05_bigwig_files/
run_times/human/06_macs3_peaks/
run_times/human/hg19/
run_times/mouse/00_logs/
run_times/mouse/paired/
run_times/mouse/01_raw_data/
run_times/mouse/02_fastqc_analysis/
run_times/mouse/03_sam_files/
run_times/mouse/mm10/
run_times/rat/00_logs/
run_times/rat/paired/
run_times/zebrafish/00_logs/
run_times/zebrafish/paired/
replicability/0*
replicability/mm9/
replicability/replicability
replicability/single/
cut_and_tag_run/00_logs/
cut_and_tag_run/01_raw_data/
cut_and_tag_run/02_fastqc_analysis/
cut_and_tag_run/03_sam_files/
cut_and_tag_run/04_bam_files/
cut_and_tag_run/05_bigwig_files/
cut_and_tag_run/06_macs3_peaks/
cut_and_tag_run/cut_and_tag
cut_and_tag_run/danRer11/
cut_and_tag_run/paired/
cut_and_tag_run/single/
cut_and_tag_run/.ipynb_checkpoints/
cut_and_tag_run/cut_and_run_pe_outputs/
cut_and_tag_run/cut_and_run_se_outputs/
cut_and_tag_run/cut_and_tag_outputs/
