Input data and normalization
The Advanced RNA-Seq plugin requires RNA-Seq input data in the form of Expression Tracks. There is no support for microarray data or the Experiment objects used by the classic Transcriptomics Analysis tools.
Expression Tracks can be created using the RNA-Seq Analysis tool with a choice of possible expression values:
- RPKM This is the expression value measured in RPKM [Mortazavi et al., 2008]:
RPKM
.
- TPM Transcripts Per Million This is computed as
, where the sum is over the RPKM values of all genes/transcripts (see
- Total counts This is all the reads that are mapped to this gene - both reads that map uniquely to the gene or its transcripts and reads that matched to more positions in the reference which were assigned to this gene.
- Unique counts This is the number of reads that match uniquely to the gene or its transcripts.
Subsections