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-
- Initial QC - removed adaptors at 3’end of fastq files
- Used MiRDeep2 Mapper process and mapped reads to HG38 genome
- 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.
- 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