Process Short-Read FASTQ Files (Bulk)

Source: R/process-short-read.R

[Deprecated]

This function is deprecated. Use mpaqt_prepare_short_reads() instead.

mpaqt_process_short_reads(fastq_1, fastq_2, index, output_dir, threads = 1L)

Arguments

fastq_1

Path to first FASTQ file (R1) for paired-end reads

fastq_2

Path to second FASTQ file (R2) for paired-end reads

index

An mpaqt_index object (bundled or with valid kallisto_index path)

output_dir

Output directory for results (default: tempdir())

threads

Number of threads for kallisto (default: 1)

Value

An mpaqt_counts_sr object (invisibly)