From aligned BAM file, compute counts per feature
Usage
BascetCountFeature(
bascetRoot,
inputName = "aligned",
outputName = "featurecount",
gffFile,
useFeature = "gene",
attrGeneId = "gene_id",
attrGeneName = "name",
overwrite = FALSE,
runner = GetDefaultBascetRunner(),
bascetInstance = GetDefaultBascetInstance()
)Arguments
- bascetRoot
The root folder where all Bascets are stored
- inputName
Name of input shard
- outputName
Name of output shard
- gffFile
GFF-like file to use for feature annotation
- useFeature
Feature type in the file to count
- attrGeneId
Attribute field to use this on for gene ID
- attrGeneName
Attribute field to use this on for gene name
- overwrite
Force overwriting of existing files. The default is to do nothing files exist
- runner
The job manager, specifying how the command will be run (e.g. locally, or via SLURM)
- bascetInstance
A Bascet instance