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Seurat.QC (v4)

Description: GenePattern module which implements the QC steps for Seurat. This is typically the first step in the Seurat Suite modules (unless you are doing batch correction, then you want to run Seurat.BatchCorrection).

Authors: Edwin Juárez and Jonathan Zamora

Contact: Forum Link

Algorithm Version: Seurat 4.0.3

Summary

The Seurat.QC Module aims to provide a quick look at some basic single-cell datasets. The resultant preprocessed dataset can then be used for downstream analyses and visualizations (such as Seurat.Preprocessing).

References

Satija Lab

Seurat

Module Repo

Module's Docker Image

Technical Notes

Uses Seurat version 4.0.3

Parameters

Name Description
input_file .tar.gz, .zip, or .loom file input that contains the raw single cell data -- currently only 10x data and .loom files from HCA are supported.
column_name column name of percent mitochondrial genes. Note: not all datasets have this column, those who do often times name it percent.mt].
pattern what pattern to use to label mitochondrial genes [often times this is annotated as MT-].
first_feature [For QC plots] First feature to plot as a violin plot [typically one of the columns in the matrix.mtx file. Sometimes named features.tsv].
second_feature [For QC plots] Second feature to plot as a violin plot [typically one of the columns in the matrix.mtx file. Sometimes named features.tsv].
third_feature [For QC plots] Third feature to plot as a violin plot [typically one of the columns in the matrix.mtx file. Sometimes named features.tsv]. Leave blank if you don't want this to be plotted.
file_name Basename of the file to be saved.
export_txt Wether or not to create a TXT file compatible with some other modules (this requires a large amount of memory and for large datasets it causes unpredicted errors).

Output Files

  1. <file_name>.rds [typically seurat_preprocessed_dataset.rds]
    • The .rds file can be used on another one of GenePattern's Seurat suite modules, such as the Seurat.Preprocessing module.
  2. <your_output_file_name>.pdf [typically Rplots.pdf]
    • The .pdf file which contains plots of the preprocessing steps.
  3. <file_name>.txt [typically seurat_preprocessed_dataset.txt]
    • The .txt file containing a dense matrix (typically a large file) that can be used on another one of GenePattern's suite modules, such as the Seurat.BatchCorrection or Conos modules.

License

Seurat.Preprocessing is distributed under a modified BSD license available at https://github.com/genepattern/Seurat.Preprocessing/blob/develop/LICENSE

Platform Dependencies

Task Type CPU Type Operating System Language
Any Any R 4.0.2

Version Comments

Version Release Date Description
4 2021-07-15 Accepting Loom files from HCA
3 2021-02-26 Updating Seurat.QC to make creation of .txt dense matrix optional (improving performance.)
1 2020-11-16 Initial Release of Seurat.QC