Set and retrieve named parameters that control the Bowtie2 alignment program.
1 2 3 4 5 6
parameters to query, or name-value pairs for setting parameters
name of a
Bowtie2 uses several command line parameters that affect its runtime behaviour,
and this utility provides a common interface to setting and retrieving those
Bowtie2 parameters. To see all current parameters, use
Required parameters at present:
Program is the full pathname to the Bowtie2 executable program
IndexPath is the pathname to the folder of all needed Bowtie2
GenomicIndex is the basename of the Bowtie2 Index to be used for
the genomic alignment phase of the pipeline
bowtie2Par.defaults() with no
optionsFile will use values from
the environment variables: BOWTIE2_PROGRAM, BOWTIE2_INDEX_PATH, and BOWTIE2_INDEX_FILE,
bowtie2Par(parameter) the currently set value of that parameter, or an error
if that parameter is not set.
getBowtie2Version(), the current version of Bowtie2 as a character string
fastqToBAM for a higher level wrapper to calling Bowtie
buildBowtie2CommandLine for the utility that constructs valid Bowtie2 command lines.
callBowtie2 for invoking the Bowtie2 alignment program.
buildBowtie2BuildCommandLine for the utility that constructs valid Bowtie2-build command lines.
callBowtie2Build for invoking the Bowtie2-build index creation program.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.