I have downloaded the miRNA Isoform expression quantification data (
mirbase21.isoforms.quantification.txt) from TCGA. The data looks like below:
miRNA_ID read_count miRNA_region hsa-let-7b 2 precursor hsa-let-7b 1 precursor hsa-let-7b 1 precursor hsa-let-7b 58 MIMAT0000063 hsa-let-7b 173 MIMAT0000063 hsa-let-7b 5723 MIMAT0000063 hsa-let-7b 26947 MIMAT0000063 hsa-let-7b 1 stemloop hsa-let-7b 1 MIMAT0004482 hsa-let-7b 2 MIMAT0004482 hsa-let-7b 129 MIMAT0004482 hsa-let-7b 401 MIMAT0004482
And based on
miRBaseConverter and information from
miRTarbase I have the mature regions 3p and 5p information with Accession like below:
miRNAName_v21 Accession hsa-let-7b-5p MIMAT0000063 hsa-let-7b-3p MIMAT0004482
So, based on above information I can sum the counts of mature 3p and 5p. And the main precursor also I can do, but what are stemloops? Do I need to include that with precursor or need to exclude that from analysis?