Quantify miRNA

The Quantify miRNA tool counts and annotates miRNAs using miRBase and performs expression analysis of the results. The tool will output two expression tables. The "Grouped on mature" table has a row for each mature miRNA. The same mature miRNA may be produced from different precursor miRNAs. The "Grouped on seed" table has a row for each seed sequence. The same seed sequence may be found in different mature miRNAs.

The algorithm first collapses identical reads into unique search sequences. This significantly reduces the number of miRNA reads in the subsequent alignment step and thereby saves computational time. The report contains values for both reads and unique search sequences.

The tool will take:

To run the tool, go to:

Toolbox | RNA-Seq and Small RNA Analysis (Image rna_seq_group_closed_16_n_p)| miRNA Analysis (Image mirna_tools_folde_open) | Quantify miRNA (Image mirna_quantification_16_n_p)

First select the trimmed reads as in figure 31.15.

Image quantifymirna1
Figure 31.18: Select the reads.

If the sequencing was performed using Spike-ins controls, the option "Enable spike-ins" can be enabled in the Quality control dialog (figure 31.16), and a spike-ins file can be specified. You can also change the Low expression "Minimum supporting count", i.e., the minimum number of supporting reads for a small RNA to be considered expressed.

Image quantifymirna2
Figure 31.19: Specifying spike-ins is optional, and you can change the threshold under which a small RNA will be considered expressed.

In the annotation dialog, several configurations are available.

In the miRBase annotations section, specify a single reference - miRBase in most cases.

miRBase can be downloaded using the Reference Data Manager under QIAGEN Sets | Reference Data Elements | mirBase (figure 31.17).

Image mirbaserefmanager
Figure 31.20: Download the latest miRBase database in the Workbench.

You can also import miRBase into the CLC Genomics Workbench using Standard Import. The miRBase data file can be downloaded from ftp://mirbase.org/pub/mirbase/CURRENT/miRNA.dat.gz. Select MiRBase (.dat) in the Force import as type menu of the Standard Import dialog. Information about the miRBase dat format is provided in miRBase data file format.

Once miRBase has been selected, click the green plus sign to see the list of species available. It can take a while for all species to load. Species to be used for annotation should be selected using the left and right arrows, and prioritized using the up and down arrows, with the species sequenced always selected as top in the priority list (figure 31.18). The naming of the miRNA will depend on this prioritization.

In addition, it is possible to configure how specific the association between the isomiRs and the reads has to be by allowing mismatches and additional or missing bases upstream and downstream of the isomiR.

Image quantifymirna3
Figure 31.21: Specify and prioritize species to use for annotation, and how stringent the annotation should be.

In the Custom databases, you can optionally add sequence lists with additional smallRNA reference databases e.g. piRNAs, tRNAs, rRNAs, mRNAs, lncRNAs. An output with quantification against the custom databases can be generated, which can be used for subsequent expression analyses.

Finally, configure the Alignment settings by defining how many "Maximum mismatches" are allowed between the reads and the references, i.e. miRBase and custom databases.

In the next dialog (figure 31.19), specify the length of the reads used for seed counting. Reads of the specified length, corresponding to the length of mature miRNA (18-25 bp by default, but this parameter can be configured) are used for seed counting. The seed is a 7 nucleotide sequence from positions 2-8 on the mature miRNA. The "Grouped on seed" output table includes a row for every seed that is observed in miRBase together with the expression of the same seed in the sample. In addition, the 20 most highly expressed novel seeds are output in the report.

Image quantifymirna4
Figure 31.22: This dialog defines the length of the reads that will be merged according to their seed.

The tool will output the following expression tables:

The expression tables can be used for subsequent expression analysis tools such as Differential Expression, PCA for RNA-Seq and Create Heat-Map for RNA-Seq. In addition, and depending on the options selected in the last dialog, the tool can output a report and a sequence list of reads that could not be mapped to any references. For a detailed description of the outputs from Quantify miRNA see Quantify miRNA outputs