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BEDstats

BEDstats is a tool that calculates the statistics of a BED file and provides plots to visualize the results.

It produces BED file Statistics:

  • GC content.The average GC content of the region set.
  • Number of regions. The total number of regions in the BED file.
  • Median TSS distance. The median absolute distance to the Transcription Start Sites (TSS)
  • Mean region width. The average region width of the region set.
  • Exon percentage. The percentage of the regions in the BED file that are annotated as exon.
  • Intron percentage. The percentage of the regions in the BED file that are annotated as intron.
  • Promoter proc percentage. The percentage of the regions in the BED file that are annotated as promoter-prox.
  • Intergenic percentage. The percentage of the regions in the BED file that are annotated as intergenic.
  • Promoter core percentage. The percentage of the regions in the BED file that are annotated as promoter-core.
  • 5' UTR percentage. The percentage of the regions in the BED file that are annotated as 5'-UTR.
  • 3' UTR percentage. The percentage of the regions in the BED file that are annotated as 3'-UTR.

Step 1: Install all dependencies

First you have to install bedboss and check if all requirements are satisfied. To do so, you can run next command: 

bedboss check-requirements
If requirements are not satisfied, you will see the list of missing packages.

Step 2: Run bedstats

Run BEDstats from command line

bedboss stats \
    --bedfile path/to/bedfile.bed \
    --outfolder path/to/output/dir \
    --genome hg38 \

Run BEDstats from within Python

from bedboss import bedstats

bedstat(
    bedfile="path/to/bedfile.bed",
    outfolder="path/to/output/dir",
    genome="hg19",
    )

After running BEDstats, you will find the following files in the output directory + all statistics will be saved in output file.