Ngs BuildPremRNAGeneModel.pdf

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Build PremRNA Gene Model


This module is specially designed to handle single-nuclei RNA-seq assay, or similar assays that are able to capture unspliced pre-mRNA as well as mature mRNA. With the normal gene model, after alignment, the quantification module will only count reads aligned to exons. Since pre-mRNA will generate intronic reads, we provide this module in ArrayStudio, during which each gene transcript was replaced as 'exon'. Thus, these intronic reads will be included in the UMI counts for each gene. This module has adopted similar logic from CellRanger to build a premRNA gene model.

Warning.png WARNING: As the transcript was replaced by exon in this new gene module, there will much longer exon in such gene model, thus, such gene model is not recommended to be used during alignment process, rather, user can use normal gene model to run the alignment, and then use premRNA gene model for the gene quantification.

To access the module, please select Analysis | NGS | Build | Build PremRNA Gene Model

NGS BuildPremRNAGeneModelMenu.png

Input Data Requirements

User should choose which genome and gene model (which are already in ArrayStudio) as input, and specifies the output name for the premRNA gene model.

If user would like to start from a GFF, GTF or BED files, user can use our Build Gene Model function to generate the omicsoft gene model first, and use this module to convert the normal gene model to be a premRNA gene model.

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General Options


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PremRNA Gene Model

  • Genome: The user must first choose the Genome to use (available genomes include any previously built genome reference).
  • Gene Model ID: The user must then choose the Gene model to use.
  • Output name: The premRNA gene model ID should be a unique and informative name that describes the gene model, and is consistent with the genome ID.
  • Append chromosome to GeneID and TranscriptID: Check this option if the same GeneID and TranscriptID can be present on multiple chromosomes (e.g. RefGene from UCSC).
    • e.g. PTPN20_10_-_2, which indicates the second instance of a gene PTPN20 on chromosome 10, in the reverse orientation.
  • Build gene and/or transcript level annotation files: Check which will be used as annotations for expression tables (like microarray type data).
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Output Results

A gene model will be built, which can immediately be used for new analyses.

If a local project is open and selected, files for the new gene model will be added to the local Omicsoft\ReferenceLibrary\(Reference_Name) folder.

If a server project is open and selected, files for the new gene model will automatically be added to the server's (Omicsoft_Directory)\ReferenceLibrary\(Reference_Name) folder.

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