MULTIseq.preProcess_allCells: MULTIseq.preProcess_allCells

In chris-mcginnis-ucsf/MULTI-seq: deMULTIplex is a software suite for MULTI-seq sample barcode FASTQ pre-processing and cell barcode classification.

MULTIseq.preProcess_allCells

Description

'MULTIseq.preProcess_allCells' reads in raw MULTI-seq sample barcode FASTQs and allocates reads into cell barcode, UMI, and sample barcode subsets. This function is a analogous to 'MULTIseq.preProcess', but is better suited for large cell ID vectors (i.e., ~10^6 total barcodes).

Usage

 MULTIseq.preProcess_allCells(R1, R2, whitelist, cell=c(1,16), umi=c(17,28), tag=c(1,8)) 

Arguments

R1	Read 1 raw FASTQ file path
R2	Read 2 raw FASTQ file path
whitelist	Cell ID whitelist used to parse R1 FASTQ file
cell	Numerical vector of length 2 specifying beginning and end position of cell barcode in R1 (Default = 1:16)
umi	Numerical vector of length 2 specifying beginning and end position of UMI in R1 (Default = 17:28)
tag	Numerical vector of length 2 specifying beginning and end position of sample tag in R2 (Default = 1:8)

Details

Requires 'ShortRead' R package.

Value

An nRead x 3 dataframe with columns correpsonding to (1) cell barcode, (2) UMI, and (3) MULTI-seq sample barcode sequences.

Author(s)

Chris McGinnis

References

Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R. ShortRead: a Bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics. 2009; 25:2607-8.

Examples

 readTable <- MULTIseq.preProcess_allCells(R1 = '/path/to/R1.fastq.gz', R2 = '/path/to/R2.fastq.gz', whitelist = cell.id.vec, cell=c(1,16), umi=c(17,28), tag=c(1,8)) 

chris-mcginnis-ucsf/MULTI-seq documentation built on Nov. 22, 2023, 8:24 p.m.