loadBEDandGenomeData: loadBEDandGenomeData

In plantformatics/Socrates: Analysis of scATAC-seq data

loadBEDandGenomeData

Description

This function loads obj 5 column BED file specifying the single-bp Tn5 integration sites. The file should not have any headers, with the following format: chromosome, start, end, barcode, strand

Usage

loadBEDandGenomeData(
  bed,
  ann,
  sizes,
  attribute = "Parent",
  verbose = T,
  is.fragment = F
)

Arguments

bed	Path to Tn5 integration site bed file with barcode information. Required.
ann	Path to GFF file for estimating % reads mapping to TSSs. Required.
sizes	Path to chromosome sizes file for downstream processing. Required.
verbose	logical. Defaults to TRUE.
is.fragment	logical. Set to TRUE if the provided BED file is the fragment.csv output from cellranger-atac count. Defaults to FALSE.

Details

The annotation file should be GFF and the chromosome sizes file should be the chromsome ID followed by its total length (e.g. chr1 123523000) with one chromosome per line.

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.