Subsections


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 33.20).

Image mirnaseed
Figure 33.20: 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 33.21). Double click on a row to open a unique reads alignment (seen at the bottom of figure 33.21). 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 33.21: 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 33.22). Double click on a row to open a unique reads alignment (seen at the bottom of figure 33.22). 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. As with the table Grouped on mature, mismatches to the reference are highlighted in the alignment and recapitulated in their name as explained in Naming isomiRs.

Image mirnacustom
Figure 33.22: Expression table grouped on custom database, with a view of a unique reads alignment.

This table contains the following information:

Report

The quantification report contains the following main sections:

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