runKallisto: run kallisto with fastq.gz files on a freshly generated or...

In RamsinghLab/arkas_staging: A package that complements Kallisto for quick, informative *seq analysis

Description

run kallisto with fastq.gz files on a freshly generated or existing index

Usage

runKallisto(sampleDir, indexName = NULL, fastaPath = ".",
  fastaFiles = NULL, fastqPath = ".", outputPath = ".",
  bootstraps = 100, threads = 4, bias = TRUE, pseudobam = FALSE,
  singleEnd = FALSE, lengthMean = 150, lengthDev = 0.001,
  collapse = "_mergedWith_", extension = ".fastq.gz", tarBall = FALSE,
  ...)

Arguments

sampleDir	character, subdirectory for sample's FASTQ files
indexName	character or NULL, optional name of the index
fastaPath	character, where FASTA files are underneath (".")
fastaFiles	character vector of FASTA transcriptomes, or NULL
fastqPath	character, where sampleDir is located under (".")
outputPath	character, output in outputPath/sampleDir (".")
bootstraps	integer, how many bootstrap replicates to run? (100)
threads	integer, how many threads to use for boot/quant? (4)
bias	boolean, perform bias correction? (TRUE)
pseudobam	boolean, produce pseudoBAM output? (FALSE)
singleEnd	boolean, produce single end quantification, mean and std.dev required
lengthMean	integer, length mean used only for single end quantification
lengthDev	integer, length std used only for single end quantification
collapse	string to name multi-FASTA indices ("_mergedWith_")
extension	string, to pass the extension into pairFastqFiles()
tarBall	boolean, gzip the output folder directory
...	any additional arguments supplied by user

RamsinghLab/arkas_staging documentation built on March 14, 2021, 11:40 a.m.