Extract IsomiR Counts

The Extract IsomiR Counts takes as input one or more "grouped on mature" expression tables, output by the Quantify miRNA tool. It extracts IsomiR composition and count information from each underlying miRNA alignment and produces tables containing this information.

If only a subset of miRNAs are of interest, we recommend creating a sample containing only the those prior to running this tool. To do this, open the expression table, select the miRNAs of interest, and click on the Create Sample from Selection (Image expression_experiment_subset) button.

If multiple expression tables are provided as input, each of the resulting isomiR counts tables will list all isomiRs that are present in any of the input samples. These result tables can be used as input to Differential Expression for RNA-Seq or Differential Expression in Two Groups to identify differentially expressed isomiRs between samples - see Differential Expression. Note that isomiR counts tables generated from different executions of Extract IsomiR Counts cannot be used together in a differential expression analysis.

Names are not always unique for isomiR sequences. If the same sequence have multiple different names, Extract IsomiR Counts write the name as a comma separated list of the different names used in the input.

To run Extract IsomiR Counts, go to:

        Toolbox | RNA-Seq and Small RNA Analysis (Image rna_seq_group_closed_16_n_p)| miRNA Analysis (Image mirna_tools_folde_open_16_n_p) | Extract IsomiR Counts (Image extract_isomirs_16_n_p)

Select one or more "grouped on mature" expression tables as input. Information from all miRNAs in this table will be extracted.

Extract IsomiR Counts output

Extract IsomiR Counts outputs a table with four columns: