detect_10x_chemistry: Auto Detect 10x Chemistry

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

Auto Detect 10x Chemistry

Description

Creates samples of 10,000 reads per lane and then determins the number of reads with barcodes in agreement with the chemistry whitelist.

Usage

detect_10x_chemistry(
  index_dir,
  data_dir,
  fqs,
  techs = c("10XV2", "10XV3"),
  threads = 1
)

Arguments

index_dir	Path to kallisto index.
data_dir	Path to folder with 10x fastq.gz files.
fqs	Vector of fastq file names.
techs	10x chemistries to check. Passed to kallisto -x argument.
threads	Number of threads to use. Default is 1.

Value

one of techs corresponding to chemistry with most reads that agree with whitelist.

hms-dbmi/drugseqr documentation built on June 24, 2024, 7:03 a.m.