miRNA seq differential analysis


I am writing to ask your help in regard to performing differential analysis to analyze miR RNA-seq data in https://usegalaxy.eu/ . I have miRNA seq data and I have analyzed in the following way-

  1. Initial QC - removed adaptors at 3’end of fastq files
  2. Used MiRDeep2 Mapper process and mapped reads to HG38 genome
  3. Then used MiRDeep2 for the identification of novel and known miRNAs. In this procedure, I used collapsed reads and mapping output (ARF format) from MiRDeep2 Mapper
    I used human mature and precursor miRNA sequences from miRBase database.
  4. I have also performed MiRDeep2 Quantifier analysis for quantitation of reads mapping to known miRBase precursors.
    Now, I would like to perform miRNA differential analysis (control vs treatment) using DESeq2. For that, I have mapped the fastq files to HG38 genome using Bowtie2 and then used featureCounts. But, the DESeq2 tool failed to perform. Could you please help me with this issue? I have also tried using MiRDeep2 Quantifier output to perform DESeq2 but failed again.

Would you be so kind to help me with this issue?

Thanks in advance


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