grada_analyze: GRADA - analyze
In LucasFVoges/GRADA: NGS data sequence (adapter) analyser

Description Usage Arguments Value

View source: R/grada_functions.R

This function will perform a unix "agrep" and "wc" to look through the read.fastq files. This will be iterativly done for each mismatch allowed (note: mismatches are only other characters - if the adapter sequence is overlaping it will not be found). The Mismatches can't be bigger then the shortest sequence!

grada_analyze(
  PE = TRUE,
  seq = NULL,
  read1 = NULL,
  read2 = NULL,
  M_min = 0,
  M_max = 2,
  output = "temp/",
  numCores = detectCores()/2
)

`PE`	paired data? TRUE / FALSE (std. TRUE)
`seq`	sequences to search for (adapters) (A text file containing:">Name Sequence IlumniaUniversalAdapter AGATCGGAAGAGC")
`read1`	Path to R1 read file (std. NULL)
`read2`	Path to R2 read file (if paired data, std. NULL)
`M_min`	minimal mismatches allowed (std. 0)
`M_max`	maximal mismatches allowed (std. 2)
`output`	the folder where all data will be created. (std. "temp/")
`numCores`	Number of cores to use. If numCores=1 then the normal lapply function is used and the parallel package is not neccessary! (std. detectCores()/2)