Ngs MirnaSeqPipeline.pdf

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miRNA-Seq Pipeline

miRNA-Seq Pipeline module allows users to finish the whole miRNA-Seq analysis in a single click. Based on user's selection, it will run the following pipeline:


After alignment, it will load BAM files once and finish all analyses.

The pipeline module is particularly better than individual modules when enable cloud based analysis with less file transfers and saving EC2 machine setup time.




Accepted file formats include FASTQ, FASTA, QSEQ, and AUTO


In the Basic section, the user has a number of options:

  • Choose a Genome and Gene model
  • File format in Gzip, Bzip2 or None
  • Replace existing BAM files in the output folder or skip the alignment step for samples already having BAM files in the output folder
  • Number of thread for each alignment and number of jobs/samples running in parallel.

Adapter Stripping

miRNAs are a class of small non-coding RNAs in length of ~22 nt. Thus, to align small RNA reads against its genome, users have to remove adapter sequences from ends of small RNA sequences. The adapter sequences are usually provided by sequence service provider.

Please read AdapterStripping_3'End for more details.


Check box to run each individual pipeline module.

Count miRNA at mature will use mature gene model for counting, such as using miRBase.R20.Mature as gene model to do counting.

Stranded counting will use /CountStrandedReads=True /CountReverseStrandedReads=False to run miRNA-Seq quantification.

Users are required to specify output name and folder.


There are multiple result data objects in Omicsoft Project:

  • NgsData objects for miRNA-Seq alignment
  • OmicData objects for Naive miRNA Count
  • Table report for raw data QC, alignment report, alignment QC


Result files in the output folder: