MULTIseq.align: MULTIseq.align

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

MULTIseq.align

Description

MULTIseq.align aligns MULTI-seq sample barcode reads to reference sequences in 10,000-cell buckets, returning sample barcode UMI count matrix.

Usage

 MULTIseq.align(readTable, cellIDs, ref) 

Arguments

readTable	An nRead x 3 dataframe with columns correpsonding to (1) cell barcode, (2) UMI, and (3) MULTI-seq sample barcode sequences, as generated by 'MULTIseq.preProcess'.
cellIDs	Vector of cellIDs which the user wants to align.
ref	Vector of reference MULTI-seq sample barcode sequences.

Details

Requires 'stringdist' R package.

Value

A MULTI-seq sample barcode UMI count matrix, including total sample barocde nUMI with and without UMI duplication adjustment. This dataframe should be used as input into the MULTI-seq sample classification workflow.

Author(s)

Chris McGinnis

References

van der Loo M. The stringdist package for approximate string matching. The R Journal. 2014; 6:111-22.

Examples

 barTable <- MULTIseq.align(readTable, cellIDs, ref) 

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