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 () 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 ()| miRNA Analysis () | Extract IsomiR Counts ()
Select one or more "grouped on mature" expression tables as input. Information from all miRNAs in this table will be extracted.
Extract IsomiR Counts outputs a table with four columns:
- Name The name of the IsomiR
- Sequence The sequence of the IsomiR
- Count The number of times the sequence was found in the sample. If UMI technology was used, this refers to the number of UMI reads the sequence was found in.
- Ambiguous A check in this column indicates that the sequence mapped to multiple entries in miRBase or multiple entries in a custom database. See Naming isomiRs for further details.