Quantify miRNA outputs

Grouped on seed

(Image rna_seeds_table_16_n_p)

In this expression table, there is a row for each seed sequence (figure 30.51).

Image mirnaseed
Figure 30.51: Expression table grouped on seed.

This table contains the following information:

Grouped on mature

(Image annotate_small_rna)

In this table, there is a row for each mature miRNA in the database, including those for which the expression is zero (figure 30.52). Double click on a row to open a unique reads alignment (seen at the bottom of figure 30.52). Unique reads result from collapsing identical reads into one. The number of reads that are collapsed into a unique read is indicated in parentheses to the right of the miR name of the unique mature read. The alignment shows all possible unique reads that have aligned to a specific miRNA from the database. Mismatches to the mature reference are highlighted in the alignment and recapitulated in their name as explained in Naming isomiRs.

Image mirnamature
Figure 30.52: Expression table grouped on mature, with a view of a unique reads alignment.

This table contains the following information:

Grouped on custom database

(Image annotate_small_rna)

In this table, there is a row for each mature smallRNA in the database, including those for which the expression is zero (figure 30.53). Double click on a row to open a unique reads alignment (seen at the bottom of figure 30.53). Unique reads result from collapsing identical reads into one. The number of reads that are collapsed into a unique read is indicated in parentheses to the right of the miR name of the unique mature read. The alignment shows all possible unique reads that have aligned to a specific miRNA from the database. Mismatches to the mature reference are expressed according to a gradient that can be changed in the Side Panel.

Image mirnacustom
Figure 30.53: Expression table grouped on custom database, with a view of a unique reads alignment.

This table contains the following information:

Reports and discarded reads

The workflow also outputs reports:

The quantification report contains the following main sections:

It is later possible to combine all reports issued for one sample using the Create Combined miRNA Report tool.