Parameter

[Czh3]

Hi,

Thanks for developing the nice tool. When I use the footprints function, I am confused with the "-r REGIONS". It needs non-peaks bed file according the help doc. But how I can get the motif footprint of the peaks of interest?

chrombpnet footprints [-h] -m MODEL_H5 -r REGIONS -g GENOME -fl CHR_FOLD_PATH -op OUTPUT_PREFIX -pwm_f MOTIFS_TO_PWM
[-bs BATCH_SIZE] [--ylim YLIM]
Input Format
required arguments:
-m MODEL_H5, --model-h5 MODEL_H5
Path model .h5 file
-r REGIONS, --regions REGIONS
10 column bed file of non-peak regions
-g GENOME, --genome GENOME
Genome fasta
-fl CHR_FOLD_PATH, --chr-fold-path CHR_FOLD_PATH
Fold information - dictionary with test,valid and train keys and values with corresponding chromosomes
-op OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX
Output prefix for bigwig files
-pwm_f MOTIFS_TO_PWM, --motifs-to-pwm MOTIFS_TO_PWM
Path to a TSV file containing motifs in first column and motif string to use for footprinting in second column

Thanks,
Chao

[panushri25]

Are you looking to make predictions in your peak regions ? You can just pass your reference genome, the region of interest and use the following script - https://github.com/kundajelab/chrombpnet/wiki/Generate-prediction-bigwigs

The motif footprint tool is to isolate the footprint of motif from the surrounding effect of other motifs.