Generate prediction bigwigs

Generate ChromBPNet predictions on given regions and output to a bigwig file.

The script chrombpnet_predict_to_bigwig can be invoked to generate bigwigs containing predictions on a set of input regions. Please provide absolute paths to this script.

Usage

chrombpnet_predict_to_bigwig [-h] -bm BIAS_MODEL -cm CHROMBPNET_MODEL -cmb CHROMBPNET_MODEL_NB -r REGIONS -g GENOME -c CHROM_SIZES -o OUT_PREFIX [-b BATCH_SIZE] [-t TQDM]  [-d DEBUG_CHR [DEBUG_CHR ...]]

-bm BIAS_MODEL, --bias-model BIAS_MODEL, Path to bias model h5
-cm CHROMBPNET_MODEL, --chrombpnet-model CHROMBPNET_MODEL
                        Path to chrombpnet model h5
-cmb CHROMBPNET_MODEL_NB, --chrombpnet-model-nb CHROMBPNET_MODEL_NB
                        Path to chrombpnet no bias model h5
-r REGIONS, --regions REGIONS
                        Must be a narrowPeak file, and must have 10 columns, with values minimally for chr, start, end and summit (10th 
                        column). Every region is centered at start + summit internally, across all regions.
-g GENOME, --genome GENOME
                        Genome fasta
-c CHROM_SIZES, --chrom-sizes CHROM_SIZES
                        Chromosome sizes 2 column tab-separated file
-o OUT_PREFIX, --out-prefix OUT_PREFIX
                        Output bigwig file
-b BATCH_SIZE, --batch-size BATCH_SIZE
-t TQDM, --tqdm TQDM  Use tqdm. If yes then you need to have it installed.
-d DEBUG_CHR [DEBUG_CHR ...], --debug-chr DEBUG_CHR [DEBUG_CHR ...]
                        Run for specific chromosomes only (e.g. chr1 chr2) for
                        debugging