sc_atac_remove_duplicates: Removing PCR duplicates using samtools
In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing
View source: R/sc_atac_remove_duplicates.R
sc_atac_remove_duplicates R Documentation
Removing PCR duplicates using samtools
Description
Takes in a BAM file and removes the PCR duplicates using the samtools markdup function. Requires samtools 1.10 or newer for statistics to be generated.
Usage
sc_atac_remove_duplicates(inbam, samtools_path = NULL, output_folder = NULL)
Arguments
inbam
The tagged, sorted and duplicate-free input BAM file
samtools_path
The path of the samtools executable (if a custom installation is to be specified)
output_folder
The path of the output folder
Value
file path to a bam file created from samtools markdup
LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.
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View source: R/sc_atac_remove_duplicates.R
| sc_atac_remove_duplicates | R Documentation |
Removing PCR duplicates using samtools
Description
Takes in a BAM file and removes the PCR duplicates using the samtools markdup function. Requires samtools 1.10 or newer for statistics to be generated.
Usage
sc_atac_remove_duplicates(inbam, samtools_path = NULL, output_folder = NULL)
Arguments
inbam |
The tagged, sorted and duplicate-free input BAM file |
samtools_path |
The path of the samtools executable (if a custom installation is to be specified) |
output_folder |
The path of the output folder |
Value
file path to a bam file created from samtools markdup
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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