decode_errors: Decode fastq

In andrewGhazi/malacoda: Bayesian Analysis of High-Throughput Genomic Assays

Description

If one of the barcodes sets from freebarcodes is used, this function can be used to decode the erroneous barcode reads.

Usage

decode_errors(trimmed_fastqs, bc_set, temp_dir, other_fb_args = "")

Arguments

trimmed_fastqs	a character string vector giving the paths to all the trimmed fastq files to be decoded
bc_set	a character string giving the path of the freebarcodes barcode set file to use for decoding
temp_dir	a character string giving the path to a directory to use for temporary intermediate files
other_fb_args	a character string giving other arguments to pass to freebarcodes (besides barcode set and output directory)

Note

See the freebarcodes github page for more details on additional arguments, the decoding process, the freebarcodes package, and their original publication (Hawkins et al, Proc Natl Acad Sci, 2018).

andrewGhazi/malacoda documentation built on Aug. 2, 2020, 12:54 a.m.