dedupByPos: Deduplication with umitools

In BMILAB/scAPAtrap: Identification and Quantification of Alternative Polyadenylation Sites from Single-cell RNA-seq Data

Deduplication with umitools

Description

Deduplication with umitools

Usage

dedupByPos(umitools.path, input, TenX = TRUE, ...)

Arguments

umitools.path	The path of the umi_tools.
input	A BAM file which needs the index file.
TenX	Logical value, TRUE for 10X data.
...	Arguments passed to other methods and/or advanced arguments. Advanced arguments: verbose If 'TRUE' basic status updates will be printed along the way. logf If not NULL, then it should be a character string denoting a file name. Then message will be written to 'logf'. notRun Default is FALSE. If 'TRUE', the Shell commands inside this function will not run but output the commad line.

Value

Output path of the deduplicated BAM file (<input>.dedup.bam).

Examples

umitools.path <- '/home/aa/miniconda2/envs/umi_tools/bin/umi_tools'
input <- './data/demo.Uniq.sorted.bam'
## Not run: 
dedupByPos(umitools.path, input)

## End(Not run)
dedupByPos(umitools.path, input, notRun=TRUE)

BMILAB/scAPAtrap documentation built on Oct. 13, 2023, 2:36 a.m.