Expression value

Please note that reads that map outside genes are counted as intergenic hits only and thus do not contribute to the expression values. If a read maps equally well to a gene and to an inter-genic region, the read will be placed in the gene.

The expression values are created on two levels as two separate result files: one for genes and one for transcripts (if the "Genome annotated with genes and transcripts" is selected in figure 26.4). The content of the result files is described in RNA-Seq results.

The Expression value parameter describes how expression per gene or transcript can be defined in different ways on both levels:

Please note that all values are present in the output. The choice of expression value only affects how Expression Tracks are visualized in the track view but the results will not be affected by this choice as the most appropriate expression value is automatically selected for the analysis being performed: for detection of differential expression this is the "Total counts" value, and for the other tools this is a normalized and transformed version of the "Total counts" as described below.