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STAR lines sequencing reads up against the genome and Salmon estimates how much of each transcript is present; they are the two most common first steps of an RNA-seq pipeline.
STAR (Spliced Transcripts Alignment to a Reference) is the ultrafast universal RNA-seq aligner described by Dobin and colleagues and used by the GDC pipeline; Salmon, from Patro and colleagues, quantifies transcript expression quickly and with correction for sequence and GC bias, using a lightweight mapping rather than full alignment. Which tool, genome build and annotation were used are provenance fields a model's training data should record, because they change the numbers.
Shares Genome builds: GRCh38 versus hg19 (GRCh37), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares TPM, FPKM and raw counts (expression units), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Genome builds: GRCh38 versus hg19 (GRCh37), Clinical NGS bioinformatics and variant interpretation, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Genome builds: GRCh38 versus hg19 (GRCh37), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares TPM, FPKM and raw counts (expression units), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Bulk RNA sequencing (RNA-seq) and the full transcriptome, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Bulk RNA sequencing (RNA-seq) and the full transcriptome, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Genome builds: GRCh38 versus hg19 (GRCh37), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.