The Extract IsomiR Counts takes as input "grouped on mature" expression table, output by the Quantify miRNA tool. It extracts IsomiR composition and count information from each underlying miRNA alignment and produces a table 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.
To run Extract IsomiR Counts, go to:
Toolbox | RNA-Seq and Small RNA Analysis ()| miRNA Analysis () | Extract IsomiR Counts ()
Select a "grouped on mature" expression table 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.