Ngs MergeZim.pdf

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Revision as of 21:08, 14 January 2020

Contents

Overview

Zero inflated matrices are OmicSoft's binary compression files of single cell count data. This data type stores single cell count data in a memory efficient manner while allow users to visualize single cell data in Array Studio and perform downstream functions. This module is designed to allow users to combine single cell count data from multiple samples so they perform visualizations and analyses on the total population of cells from different replicates or biological conditions.

This module can be accessed by going to NGS | SingleCell RNA-Seq | SCTools | Merge Zim:

MergeZimMenu.png

Input Data Requirements

Data (Zim files) can be generated using the Array Studio Single Cell Pipeline or from data that has been imported from other sources using popular file types (such as mtx files from Cell Ranger: Import Single Cell Counts). General Options

MergeZimGUI2.png

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Options

Users can search for all zim files that the would like to merge (i.e. individual samples or batches) and use the Add button to add to the File names section 

   Options
       Genome and Gene Model: Users can select these options if they would like to append the GeneIDs in the resulting annotation table with OmicSoft provided (or custom) annotations
       Output name: Users can select what the name of the merged zim object will be
       Output folder: can be specified for the location to store the output file.
       Rpm Scaling: If raw counts are provided, this would merge the raw data from the samples provided, as well as provide a per cell normalization scaling counts per cell to be one million.

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Output

Data will be merged into a larger ZIM file in the output folder and an object will be added to the solution explorer to view the merged data. Design and annotation tables can be added to the data object(s) - in the example below Objects ZeroInflatedData and ZeroInflatedData_2 were merged to have a total of 7746 cells in the same object, raw and Rpm normalized counts:

MergedZimOutput.png

Oscript

Ngs_MergeZim.oscript

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