Star mapping transcriptome reads - gws_omix

Typing name : TASK.gws_omix.STARMappingTranscriptomeReads

Brick : gws_omix

STARMappingTranscriptomeReads class. Represents a process that wraps STAR program.

Mapping is done on the whole genome sequence but only reads overlapping gene feature are kept.

--> THIS BAM OUTPUT FOLDER !!! IS !!! COMPATIBLE WITH SALMON QUANTIFICATION TOOL (see SalmonQuantStar class) <---

Configuration options * threads: Multi threading options: number of threads to use (min=1, max=7). [Default = 2]. * memory: Memory (RAM in Bytes) usage in Bytes. [Default = 4000000000 bytes (=4GB)].

Input

Folder_fastq_files

Folder containing all RNAseq sequecing files (fastq.gz)

Fastq folder

STAR_index_folder

Folder containing STAR index files

Folder

Metadata File

File

Output

Mapping_output_files

Mapping output file(s) (BAM format) contained in a Folder

Folder

Configuration

threads

Optional

Number of threads [Default = 2]

Type : int

Default value : 2

memory

Optional

Memory (RAM in Bytes) usage

Type : int

Default value : 6000000000