miRNA alignment on Bowtie2/miRDeep

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I was using a public RNA-Seq dataset and was exploring the insights and saw that the miRNA had very low counts compared to the other RNAs and it is logical, I was using STAR with gencode fasta file and gtf files

So, I was trying to use bowtie and miRdeep for alignment using miRbase fasta and gtf files to enrich and focus on the miRNAs in my dataset and I keep getting zero alignments and I am using the default settings wanting to retrieve only the miRNA sequences

Is there a way to solve this ?

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Welcome @Daghshy

Thanks for explaining the situation. From a first guess, the issue is either the reference data, or the alignment parameters, or the mapping tool choice.

We have an example in this tutorial – maybe it helps to frame the analysis space?

Then this shared history is the tutorial workflow and data as a more hands on example of how it all processes together.

Please give that a review and let us know if it helps or not! We can follow up more too. :slight_smile: