mapping_bowtie2: Mapping of fastq-files
In Moritz-Kohls/virDisco2: Virus Discovery

Description Usage Arguments Value Examples

The simulated fastq-files are used to be mapped against the artificial viral reference genome with bowtie2. After this step, one can filter out reads with a low mapping quality. The new sam-file with filtered reads is stored separately in the same directory.

mapping_bowtie2(
  file_indices = rep(NA_integer_, 0),
  reference_genome_index_bowtie2.directory,
  mapq_filter_threshold = 0,
  threads
)

`file_indices`	Indices of the simulated fast-file pairs that will be mapped.
`reference_genome_index_bowtie2.directory`	# Prefix (folder) of bowtie2 index files
`mapq_filter_threshold`	# Reads with a mapping quality below this threshold will be deleted from the sam-files.
`threads`	Number of threads that are used for mapping

None

library(rChoiceDialogs)
my.prefix = rchoose.dir() # Choose prefix (folder) of reference genome bowtie2 index files
my.prefix = gsub("\\\\","/",my.prefix)
my.prefix = paste0(my.prefix,"/")
mapping_bowtie2 ( file_indices = 1 , reference_genome_index_bowtie2.directory = my.prefix , mapq_filter_threshold = 2 , threads = 2 ) # Takes a few seconds to run!