get_bowtie2_cmd: Wrapper to build up the Bowtie2 command
In jkruppa/viralDetectTools: Modules for a viral detection pipeline
Description
Usage
Arguments
Details
Value
Author(s)
Description
Wrapper function to build up the Bowtie2 command for the the system() call
Usage
1
2
get_bowtie2_cmd(inFile, samOutFile, referenceDir, method, p = 32,
all = FALSE)
Arguments
inFile
File path to the in file(s)
samOutFile
Path to the sam output file
referenceDir
Path to the reference dir
method
Should ene-to-end or lcal mapping be used?
p
Number of used cores
all
Shoul the reads mapped to all possible positions on the reference [default = FALSE]
Details
This function is running internally in the map_dna_ref.
Value
character
Author(s)
Jochen Kruppa
jkruppa/viralDetectTools documentation built on May 30, 2019, 3:41 p.m.
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Description Usage Arguments Details Value Author(s)
Description
Wrapper function to build up the Bowtie2 command for the the system() call
Usage
1 2 | get_bowtie2_cmd(inFile, samOutFile, referenceDir, method, p = 32,
all = FALSE)
|
Arguments
inFile |
File path to the in file(s) |
samOutFile |
Path to the sam output file |
referenceDir |
Path to the reference dir |
method |
Should ene-to-end or lcal mapping be used? |
p |
Number of used cores |
all |
Shoul the reads mapped to all possible positions on the reference [default = FALSE] |
Details
This function is running internally in the map_dna_ref.
Value
character
Author(s)
Jochen Kruppa
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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