Question: Analysis of MiRDeep2 and DESeq2
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gravatar for guq4602
14 months ago by
guq46020
guq46020 wrote:

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.

using miRDeep2

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.

sequencing rna-seq alignment R • 599 views
ADD COMMENTlink modified 12 months ago by h.mon32k • written 14 months ago by guq46020

and I wonder if the reason for collapse is just a process to reduce computing power.

ADD REPLYlink written 14 months ago by guq46020
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