convert.bam {chicane}

convert.bam

Description

Convert a BAM file to a format that can be used for replicate merging.

Note: This function does not process data enough to be used for interaction calling. Use prepare.data for full preprocessing.

Usage

convert.bam(bam, baits, fragments, temp.directory = NULL, keep.files = FALSE)

Arguments

bam

Path to a BAM file

baits

Path to a BED file containing the baits

fragments

Path to a BED file containing all restriction fragments in the genome

temp.directory

Directory where temporary files should be stored. Defaults to current directory.

keep.files

Logical indicating whether to keep temporary files

Author(s)

Erle Holgersen <[e-mail]>

See Also

prepare.data