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        "description": "# CovFuzze Plot\nA python script to plot gene coverage and IP peaks with standard deviations calculated from multiple replicates. \n\nusage: gene_peak_plot.py [-h] [-g GENE] [-o OUT] --bams BAMS [BAMS ...] --bed \n                         BED [--gtf GTF] [-p PEAKS] -l LABELS [LABELS ...]\n                         [-n NSUBPLOTS] [--normalize]\n\n## dependencies:\n- numpy, tested with 1.11.1\n- pysam, tested with 0.9.1\n- pandas, tested with 0.18.1\n- seaborn, tested with 0.7.1 \n- matplotlib, tested with 2.0.2\n- pybedtools, tested with 0.7.10 - requires bedtools available in path\n\n## required arguments:\n```\n  -o OUT, --out OUT     output prefix (incl. dir) \n  --bams BAMS [BAMS ...] \n                        bam files (separated by spaces) \n  --bed BED             bed file for region(s) of interest  \n  -l LABELS [LABELS ...], --labels LABELS [LABELS ...] \n                        labels associated with bams - if replicates, use same \n                        labels\n```\n## optional arguments:\n```\n  -h, --help            show this help message and exit \n  -g GENE, --gene GENE  gene name (default = GeneDoe) \n  --gtf GTF             gtf file for gene to plot exons as shaded regions \n  -p PEAKS, --peaks PEAKS \n                        bed file with peaks\n  -n NSUBPLOTS, --nsubplots NSUBPLOTS \n                        number of subplots- bams will be split evenly based on \n                        the order given (default = 1) \n  --normalize           normalize by gene length/summed coverage (default = \n                        False)\n```\n\n## Example:\n```\ncovfuzze.py -o $outdir/$prefix --bams \n    alignments/sample_1_Input.sample.star.bam alignments/sample_1_IP.sample.star.bam \n    alignments/sample_2_Input.sample.star.bam alignments/sample_2_IP.sample.star.bam \n    alignments/sample_3_Input.sample.star.bam alignments/sample_3_IP.sample.star.bam \n    --bed ${gene}_exons.bed \n    -l sample_Input sample_IP sample_Input sample_IP sample_Input sample_IP \n    --gene ${gene} -n 1 --normalize\n```\n",
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