miRNA featureCounts

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1

Hello everyone
I am working in Galaxy with miRNAs data.
I am trying to pass my reads mapped with Bowtie to counts with the featureCounts app.

I have not been successful, the process gives me an error because the miRBase annotation file is in gff3 format and featureCounts asks for this file in GTF file.
How can I solve this step?

P.S. I have used the miRBase sequences to map my reads.

2

Hi @andres2r89,
I suggest you use the miRDeep2 tool for quantifying miRNAs data; it is built on Bowtie and specifically designed for working on miRNA. You can find some information about how to quantify miRNAs in this tutorial.

Regards

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