Extract barcodes and trim input raw FASTQ
Usage
BascetGetRaw(
bascetRoot,
rawmeta,
maxShardSize = "50g",
outputName = "debarcoded",
outputNameIncomplete = "incomplete_reads",
chemistry = c("atrandi-wgs", "atrandi-rnaseq", "parse-bio"),
subchemistry = NULL,
barcodeTolerance = NULL,
numLocalThreads = NULL,
bufferSize = 4000,
sortBufferSize = 4000,
overwrite = FALSE,
runner = GetDefaultBascetRunner(),
bascetInstance = GetDefaultBascetInstance()
)Arguments
- bascetRoot
The root folder where all Bascets are stored
- rawmeta
Metadata for the raw FASTQ input files. See DetectRawFileMeta
- maxShardSize
Estimated maximum size of output shard. Can be set higher but as sorting is also performed during sharding, it can be overall more efficient to only do partial sorting during this command
- outputName
Name output files: Debarcoded reads
- outputNameIncomplete
Name of output files: Reads that could not be parsed
- chemistry
The type of data to be parsed
- barcodeTolerance
Optional: Number of mismatches allowed in the barcode for it to still be considered valid
- numLocalThreads
Number of threads to use per job. Default is the number from the runner
- runner
The job manager, specifying how the command will be run (e.g. locally, or via SLURM)
- bascetInstance
A Bascet instance