GetBarcodes: Get single-cell barcodes from long read files

In noush-joglekar/scisorseqr: Processes long reads for differential isoform analysis

Get single-cell barcodes from long read files

Description

This is an R-wrapper for a python function. It parallelizes the reading and processing of fastq.gz files, and uses a sliding window approach to identify cell barcodes, assign cluster labels and output useful statistics in one .csv file and one _summary file per fastq.gz input file

Usage

GetBarcodes("FastqFolder","Barcode-Clust","~/MyDir/",6,
concatenate = FALSE,filterReads = FALSE)

Arguments

fqFolder	Path to a folder containing fastq.gz files
BCClustAssignFile	tab separated file containing barcode in column 1 and cluster in column 2
outputFolder	OPTIONAL Path to working directory. Defaults to current
numProcesses	Number of chunks to split processing into. Defaults to 10
chemistry	UMI length differs with 10x chemistry. Defaults to "v2"
concatenate	OPTIONAL Concatenate output from all files in the folder
filterReads	OPTIONAL logical indicating whether the barcoded reads should be filtered into a separate file. Will make the downstream analysis faster if you expect few barcoded reads (~40 of total) at the cost of a slow (single-threaded) filtering process

Value

OutputRaw folder containing a .csv file and summary stats for each input fastq.gz file

OutputFiltered Filtered file with one line for each read containing a barcode. Option to concatenate into one file per input folder

noush-joglekar/scisorseqr documentation built on March 18, 2023, 8:06 p.m.