Sanity

Sampling Noise based Inference of Transcription ActivitY : Filtering of Poison noise on a single-cell RNA-seq UMI count matrix

Single-cell RNA sequencing normalization algorithm presented in the publication Bayesian inference of gene expression states from single-cell RNA-seq data - J Breda, M Zavolan, E van Nimwegen - Nature Biotechnology, 2021.

Sanity infers the log expression levels x_gc of gene g in cell c by filtering out the Poisson noise on the UMI count matrix n_gc of gene g in cell c.

Reproducibility

The raw UMI count and normalized datasets mentionned in benchmarking in the associated publication are available on . Files are named [dataset name]_UMI_counts.txt.gz and [dataset name]_[tool name]_normalization.txt.gz.

The scripts used for running the bechmarked normalization methods and for making the figures of the preprint are in the reproducibility folder.

Input

• UMI count matrix: (N_g x N_c) matrix with N_g the number of genes and N_c the number of cells. Format: tab-separated, comma-separated, or space-separated values. ('path/to/text_file')

GeneID	Cell 1	Cell 2	Cell 3	...
Gene 1	1.0	2.0	0.0
Gene 2	6.0	3.0	1.0
...

• (Alternatively) Matrix Market File Format: Sparse matrix of UMI counts. Automatically recognized by .mtx extension of the input file. Named matrix.mtx by cellranger 2.1.0 and 3.1.0 (10x Genomics). ('path/to/text_file.mtx')
  • (optional) Gene ID file: Named genes.tsv by cellranger 2.1.0 and features.tsv by cellranger 3.1.0 (10x Genomics). ('path/to/text_file')
  • (optional) Cell ID file: Named barcodes.tsv by cellranger 2.1.0 and 3.1.0 (10x Genomics). ('path/to/text_file')
• (optional) Destination folder ('path/to/output/folder', default: pwd)
• (optional) Number of threads (integer, default: 4)
• (optional) Print extended output (Boolean, 'true', 'false', '1' or '0', default: false)
• (optional) Minimal and maximal considered values of the variance in log transcription quotients (double, default: v_min=0.001 v_max=50)
• (optional) Number of bins for the variance in log transcription quotients (integer, default: 160)
• (optional) Option to skip cell size normalization (Boolean, 'true', 'false', '1' or '0', default: false)

Output

• log_transcription_quotients.txt: This file contains the estimated values of the log-transcription quotients (LTQs) for each gene in each cell. The LTQ x_gc of gene g in cell c corresponds to the estimated logarithm of the fraction of mRNAs in cell c that belong to gene g. The LTQs are thus normalized such that Σ_g exp(x_gc) = 1 for each cell c. In order to get an estimate of the number of mRNAs for gene g in cell c one would thus need to multiply exp(x_gc) by the estimated total number of mRNAs M in the cell.

  GeneID	Cell 1	Cell 2	Cell 3	...
  Gene 1	-13.7227	-13.722	-13.729
  Gene 2	-9.96744	-10.2522	-10.1453
  ...

• ltq_error_bars.txt : Table with the error-bars on the estimates of the LTQs x_gc for each gene g in each cell c.

  GeneID	Cell 1	Cell 2	Cell 3	...
  Gene 1	0.630111	0.630198	0.624802
  Gene 2	0.315551	0.325912	0.301861
  ...

Extended output (optional)

• mu.txt : Estimated average LTQ μ_g of each gene g (averaged over all cells)

• d_mu.txt : Error bars on the inferred mean LTQs μ_g.

• variance.txt : Estimated variance of the LTQs x_gc across cells c for each gene g. Note that these variances are different, and generally larger, than what one would obtain when directly calculating the variance of the estimates of x_gc from the file log_transcription_quotients.txt. This is because the estimates in this file take into account the uncertainty on the estimates of the x_gc. Thus, when estimates of true gene expression variability are needed, you are strongly adviced to use the results in this file.

• delta.txt : Matrix of inferred log-fold changes δ_gc = x_gc-μ_g for each gene g in each cell c.

• d_delta.txt : Matrix of error-bars for the inferred log fold-changes δ_gc.

• likelihood.txt : This file encodes the posterior distribution of each gene’s true variance in log-expression. For the numerical calculation of this distribution, the variance is a prior assumed to lie in the range [v_min,v_max] and is discretized into N_b bins uniformly on a logarithmic scale. The file contains the matrix with posterior values P_gb for each gene g and each bin b.

  Variance	0.01	0.0107	0.0114	...
  Gene 1	0.018	0.019	0.020
  Gene 2	0.0006	0.0051	0.0031
  ...

Usage

  ./Sanity <option(s)> SOURCES
  Options:
	-h,--help		Show this help message
	-v,--version		Show the current version
	-f,--file		Specify the input transcript count text file (.mtx for Matrix Market File Format)
	-mtx_genes,--mtx_gene_name_file	Specify the gene name text file (only needed if .mtx input file)
        -mtx_cells,--mtx_cell_name_file	Specify the cell name text file (only needed if .mtx input file)
	-d,--destination	Specify the destination path (default: pwd)
	-n,--n_threads		Specify the number of threads to be used (default: 4)
	-e,--extended_output	Option to print extended output (default: false, choice: false,0,true,1)
	-vmin,--variance_min	Minimal value of variance in log transcription quotient (default: 0.001)
	-vmax,--variance_max	Maximal value of variance in log transcription quotient (default: 50)
	-nbin,--number_of_bins	Number of bins for the variance in log transcription quotient  (default: 160)
	-no_norm,--no_cell_size_normalization	Option to skip cell size normalization (default: false, choice: false,0,true,1)

Installation

• Clone the GitHub repository

git clone https://github.com/jmbreda/Sanity.git

• Install OpenMP library

  • On Linux
    If not already installed (Check with ldconfig -p | grep libgomp, no output if not installed), do

   sudo apt-get update
   sudo apt-get install libgomp1
  

  • On mac OS using macports
    Install the gcc9 package

   port install gcc9
  

         Change the first line of src/Makefile from CC=g++ to CC=g++-mp-9

  • On mac OS using brew
    Install the gcc9 package

   brew install gcc9
  

         Change the first line of src/Makefile from CC=g++ to CC=g++-9

• Move to the source code directory and compile.

cd Sanity/src
make

• The binary file is located in

Sanity/bin/Sanity

• Alternatively, the already compiled binary for macOS is located in

Sanity/bin/Sanity_macOS

Sanity_distance

Compute cell-cell distances from Sanity output files. Needs extended outputs of Sanity (-e 1 option).

Input

• The output folder of the Sanity run, specifiied with the -d option in Sanity ('path/to/folder')
• (optional) The gene signal to noise ratio used as gene cut-off (double, default: 1.0)
• (optional) Compute distances with or without errorbars (boolean, default: 1 or true)
• (optional) Number of threads (integer, default: 4)

Output

• Cell-cell distance: (N_c(N_c-1)/2) vector of cell to cell distances dist(cell_i,cell_j), i=1,...,N_c-1, j=i+1,...,N_c, with N_c the number of cells.

  dist(cell1,cell2)
  dist(cell1,cell3)
  dist(cell1,cell4)
  ...
  dist(cellNc-2,cellNc-1)
  dist(cellNc-2,cellNc)
  dist(cellNc-1,cellNc)

located in the Sanity output folder (specified with -f option), named cell_cell_distance_[...].txt, depending on the -err and -s2n options.

Usage

./Sanity_distance <option(s)> SOURCES
Options:
	-h,--help		Show this help message
	-v,--version		Show the current version
	-f,--folder		Specify the input folder with extended output from Sanity
	-s2n,--signal_to_noise_cutoff	Minimal signal/noise of genes to include in the distance calculation (default: 1.0)
	-err,--with_error_bars	Compute cell-cell distance taking the errobar epsilon into account (default: true)
	-n,--n_threads		Specify the number of threads to be used (default: 4)

Instalation

Same dependencies as Sanity (see above).

• Move to the source code directory and compile.

cd Sanity/src
make Sanity_distance

• The binary file is located in

Sanity/bin/Sanity_distance

Help

For any questions or assistance regarding Sanity, please post your question in the issues section.