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BEDboss

bedboss is a command-line pipeline that standardizes and calculates statistics for genomic interval data, and enters the results into a BEDbase database. It has 3 components:

1) bedmaker (bedboss make);
2) bedqc (bedboss qc);
3) bedstat (bedboss stat);
4) bedbuncher (bedboss bunch).

You may run all 3 pipelines together, or separately.

Mainly pipelines are intended to be run from command line but nevertheless, they are also available as a python function, so that user can implement them to his own code.


BEDboss consist of 3 main pipelines:

bedmaker

bedmaker - pipeline to convert supported file types* into BED format and bigBed format. Currently supported formats:

  • bedGraph
  • bigBed
  • bigWig
  • wig

bedqc

flag bed files for further evaluation to determine whether they should be included in the downstream analysis. Currently, it flags bed files that are larger than 2G, has over 5 milliom regions, and/or has mean region width less than 10 bp. This threshold can be changed in bedqc function arguments.

bedstat

pipeline for obtaining statistics about bed files

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.

bedbuncher

Pipeline designed to create bedsets (sets of BED files) that will be retrieved from bedbase.

Example bedsets: - Bed files from the AML database. - Bed files from the Excluderanges database. - Bed files from the LOLA database.

Bedbuncher calculates statistics: - Bedset statistics (currenty means and standard deviations).


Additional information

bedmaker

Additional dependencies

  • bedToBigBed: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed
  • bigBedToBed: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed
  • bigWigToBedGraph: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph
  • wigToBigWig: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig

bedstat

Additional dependencies

regionstat.R script is used to calculate the bed file statistics, so the pipeline also depends on several R packages:

All dependencies you can find in R helper script, and use it to easily install the required packages: