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BEDqc tutorial

BEDqc

BEDqc is a tool for quality control of BED files. As for now, it checks: - maximum file size, - maximum number of regions, - minimum region width threshold

Run BEDqc from command line

bedboss qc \
    --bed-file path/to/bedfile.bed \
    --outfolder path/to/output/dir

Run BEDqc from within Python 

from bedboss import bedqc

bedqc.run_bedqc(
    bedfile="path/to/bedfile.bed",
    outfolder="path/to/output/dir"
    max_file_size=1000000, # optional
    max_number_of_regions=1000, # optional
    min_region_width=10, # optional
)

If file won't pass the quality control, it will raise an error. and add this information to the log file.