I want a pipeline for expression profiling and will proceed with DEanalysis later. I found the pipeline while i was searching for miRNA-seq data analysis.
mapper.pl input(fastq) -e -h -j -m -s output quantifier.pl -p (Ref_hairpin from miRBase) -m (Ref_mature from miRBase) -r mapper.pl output) -t hsa -g 2 -e 2 -f 5
It was a pipeline that made a table by combining the ABC files obtained in this way and proceeded with DEanalysis using DESeq2.
miRNA read_count precursor total seq seq(norm) hsa-let-7a-5p 597882 hsa-let-7a-1 597882 597882 47424.19 hsa-let-7a-3p 29 hsa-let-7a-1 29 29 2.3
I think.. use the read_count value to run DESeq2......
I would like to get help because it is not mentioned why there is no mapping process in reference genome. And I'm wondering if it's right to analyze it like this pipeline.