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Introduction Version

Salmon quant mapping

TASK
Typing name :  TASK.gws_omix.SalmonQuantMapping Brick :  gws_omix v

SalmonQuantMapping class. Represents a process that wraps Salmon pseudo-aligment RNAseq mapping program (salmon quant).

Configuration options * threads: Multi threading options: number of threads to use (min=2). [Default = 2].

Input

FastqFolder
Fastq Folder containing all RNA-sequencing file
MetadataFile
File containing metadata information link to file and sample (see Gencovery hub documentation at: https://hub.gencovery.com/bricks/gws_omix/latest/doc/use-cases/undefined )
SalmonIndex
Folder containing Salmon index files

Output

TpmCountFile
Tpm genes expression counting files merged in one (see salmon quantmerge documentation)
RawCountFile
Raw count genes expression counting files merged in one (see salmon quantmerge documentation)

Configuration

threads

Optional

Number of threads [Default = 2]

Type : intDefault value : 2