sort_index_idxstats_bam: Sorts, indexes the BAM file, and retrieves the 'idxstats'.

In HarteminkLab/TOP: Predict transcription factor occupancy using DNase- or ATAC-seq data

Sorts, indexes the BAM file, and retrieves the idxstats.

Description

Sorts and indexes the BAM file, and retrieves the idxstats (summary of the number of mapped reads on every chromosome) using Rsamtools package.

Usage

sort_index_idxstats_bam(
  bam_file,
  sorted_bam_file,
  sort = TRUE,
  index = TRUE,
  idxstats = TRUE
)

Arguments

bam_file	Input BAM file.
sorted_bam_file	Output file name for sorted BAM file if sort=TRUE.
sort	Logical. If TRUE, sorts the BAM file.
index	Logical. If TRUE, indexes the BAM file.
idxstats	Logical. If TRUE, retrieves idxstats summary of the number of mapped reads in each chromosome.

Examples

## Not run: 
# Sorts, indexes the BAM file, and retrieves the idxstats.
sort_index_idxstats_bam('example.bam', sort=TRUE, index=TRUE, idxstats=TRUE)

# Indexes the BAM file, and retrieves the idxstats, using sorted BAM file.
sort_index_idxstats_bam('example.sorted.bam', sort=FALSE, index=TRUE, idxstats=TRUE)

## End(Not run)

HarteminkLab/TOP documentation built on July 27, 2023, 6:14 p.m.