scReadSim source code

The source code for the reproduction of results in "scReadSim: a single-cell RNA-seq and ATAC-seq read simulator".

Software scReadSim

We provide a Python-based implementation for the convenience of the community. For tutorials and other details, check our website.

Usage instructions

Four folders correspond to four tasks:

• 10x_scRNA-seq: Using 10x scRNA-seq for synthetic read generation, verification, and benchmarking of deduplication tools
• 10x_scATAC-seq: Using 10x scATAC-seq for synthetic read generation and verification
• sci-ATAC-seq: Using sci-ATAC-seq for synthetic read generation and verification
• sci-ATAC-seq_designedpeaks: Using sci-ATAC-seq for synthetic read generation with designed ground-truth peaks, verification, and benchmarking of peak calling tools

Under each folder, Synthetic data generation contains codes for generating synthetic reads and Verification contains codes for reproducing the figures in the manuscript. A detailed list is as follows.

Task: 10X_scATAC-seq

Folder Synthetic data generation

Code	Function
NOINPUT_ATAC_main_20221130_GreyArea.sh	main script
NOINPUT_ATAC_BAM2CountMatrix.py	convert BAM file to count matrix
NOINPUT_ATAC_ComplePeakFunction.py	prepare scATAC-seq non-peaks
NOINPUT_ATAC_GenerateBAMCoord_20221130_GreyArea.py	generate synthetic read coordinates
NOINPUT_ATAC_ReadError_20220421.py	introducing sequencing errors to synthetic reads
NOINPUT_ATAC_SyntheticMat.R	synthetic count matrix generation
NOINPUT_ATAC_VerifyRead_20221130.py	calculate pseudo-bulk read coverage for each feature

Folder Verification

Code	Function
Fig2bBtmS7c_ATAC_VerifyRead_Peak_MakePlot_Nversion_20230316.R	Figs. 2b Bottom and S7c
Fig2bUpMidS7b_ATAC_VerifyRead_MakePlot_Nversion.20230316.R	Figs. 2b Upper, Middle and S7b
FigS4_ATAC_VerifyCount_20230128.R	Fig. S4

Task: 10X_scRNA-seq

Folder Synthetic data generation

Code	Function
NOINPUT_RNA_main_20221011_UMItranscriptlevel2.sh	main script
NOINPUT_RNA_main_VaryRDandCN_20221013.sh	main script for varying cell number and sequencing depth
NOINPUT_RNA_BAM2CountMatrix_20220928.py	convert BAM file to count matrix
NOINPUT_RNA_ComplePeakFunction_20220603.py	prepare scRNA-seq features
NOINPUT_RNA_GenerateBAMCoord_20221011_UMITranscriptLevel2.py	generate synthetic read coordinates
NOINPUT_RNA_ReadError_20220421.py	introducing sequencing errors to synthetic reads
NOINPUT_RNA_SyntheticMat.R	synthetic count matrix generation
NOINPUT_RNA_SyntheticUMIMat_VaryRDandCN_20221013.R	synthetic count matrix generation for varying cell number and sequencing depth
NOINPUT_RNA_VaryRDandCN_DownsampleBAM_20221013.R	downsample cells for varying cell number

Folder Verification

Code	Function
Fig1c_RNA_Minnow_20230306.sh	Fig. 1c run minnow
Fig1c_RNA_Minnow_PrepareCountMatrix.R	Fig. 1c prepare minnow input
Fig1c_RNA_Minnow_PlotCoverage_20230316.py	Fig. 1c
Fig2defg_RNA_VerifyPipeline_20230315_withoutAlevin_Nversion.R	Fig. 2defg
Fig2defg_RNA_VerifyPipeline_CellRanger_20221011_UMItranscriptlevel2.sh	Fig. 2defg run cellranger
Fig2defg_RNA_VerifyPipeline_TimeComp_CellRanger_20221015.sh	Fig. 2defg time usage benchmark of cellranger
Fig2defg_RNA_VerifyPipeline_TimeComp_UMItools_20221015.sh	Fig. 2defg time usage benchmark of UMI-tools
Fig2defg_RNA_VerifyPipeline_UMITools_20221011_UMItranscriptlevel2.sh	Fig. 2defg run UMI-tools
FigS2_RNA_VerifyCount_20230128.R	Fig. S2
FigS3_RNA_VerifyRead_MakePlot_20221017.R	Fig. S3
FigS12S13_RNA_VerifyPipeline_20230315_withAlevin_Nversion.R	Figs. S12 and S13
FigS12S13_RNA_VerifyPipeline_Alvein_20221011_UMItranscriptlevel2.sh	Figs. S12 and S13 run alevin
FigS12S13_RNA_VerifyPipeline_TimeComp_Alevin_20221015.sh	Figs. S12 and S13 time usage benchmark of alevin

Task: sci-ATAC-seq

Folder Synthetic data generation

Code	Function
NOINPUT_ATAC_main_20221130_GreyArea.sh	main script
NOINPUT_ATAC_BAM2CountMatrix.py	convert BAM file to count matrix
NOINPUT_ATAC_ComplePeakFunction.py	prepare scATAC-seq non-peaks
NOINPUT_ATAC_GenerateBAMCoord_20221130.py	generate synthetic read coordinates
NOINPUT_ATAC_ReadError_20220421.py	introducing sequencing errors to synthetic reads
NOINPUT_ATAC_SyntheticMat.R	synthetic count matrix generation
NOINPUT_ATAC_VerifyRead_20221130.py	calculate pseudo-bulk read coverage for each feature

Folder Verification

Code	Function
Fig1deS6_ATAC_SCAN-ATAC-Sim_20230303.sh	Figs. 1de and S6 run SCAN-ATAC-Sim
Fig1deS6_ATAC_SCAN-ATAC-Sim_CompareCountMat_20230310.R	Figs. 1de and S6
Fig1deS6_ATAC_SCAN-ATAC-Sim_CountMat_20230310.py	Figs. 1de and S6 generate count matrices for comparison
Fig2a_ATAC_SpitCellType_20230310.sh	Fig. 2a
Fig2b_ATAC_SpitCellType_20230310.py	Fig. 2b
FigS5_ATAC_VerifyCount_20230128.R	Fig. S5
FigS8_ATAC_VerifyRead_MakePlot_20221130.R	Fig. S8
FigS8_ATAC_VerifyRead_Peak_MakePlot_20221130.R	Fig. S8 peak calling comparison

Task: sci-ATAC-seq_designedpeaks

Folder Synthetic data generation

Code	Function
INPUT_ATAC_main_mm9TSS_20221130_GreyArea.sh	main script
INPUT_ATAC_BAM2CountMatrix.py	convert BAM file to count matrix
INPUT_ATAC_ComplePeakFunction.py	prepare scATAC-seq non-peaks
INPUT_ATAC_demoInputPeak.py	design ground-truth peaks
INPUT_ATAC_GenerateBAMCoord_20221130.py	generate synthetic read coordinates
INPUT_ATAC_MatchPeakFunction_20220302.py	match ground truth (non)peaks and trust worthy (non)peaks
INPUT_ATAC_SyntheticMat_withCluster_SelectCellType.R	synthetic count matrix generation
NOINPUT_ATAC_ReadError_20220421.py	introducing sequencing errors to synthetic reads
NOINPUT_ATAC_VerifyRead_20221130.py	calculate pseudo-bulk read coverage for each feature

Folder Verification

Code	Function
Fig2hiS10S14S15_ATAC_VerifyRead_TSS_ProcessPeakBed_20221130.sh	Figs. 2hi, S10, S14 and S15 run peak calling tools
Fig2hiS10_ATAC_VerifyRead_TSS_MakePlot_Nversion_20230316.R	Figs. 2hi and S10
FigS14S15_TSS_Intervene_upset_logTransformation_20221009.R	Figs. S14 and S15

License

This pacakge is licensed under the terms of the MIT License.