Supplementary Information:
scPipe: a flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data

Luyi Tian^{1, 2}, Shian Su¹, Xueyi Dong^1,3,
Daniela Amann-Zalcenstein¹, Christine Biben¹, Azadeh Seidi⁴,
Douglas J. Hilton^1,2, Shalin H. Naik^1,2 and Matthew E. Ritchie^1,2,5

1. Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
2. Department of Medical Biology, The University of Melbourne, Parkville, Australia
3. College of Life Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang Province, 310058, P.R. China.
4. Australian Genome Research Facility, Parkville, Australia
5. School of Mathematics and Statistics, The University of Melbourne, Parkville, Australia.

CEL-Seq2 example

Data

For demonstrative purposes the data has been subsampled to 1GB.

The full experiment is available at: GSE109999

CB51_R1.fastq.gz

CB51_R2.fastq.gz

Aligned with Subread

R script for building index and downloading annotation

R script for processing

Aligned with STAR

R script for building index and downloading annotation

R script for processing

Example Report

Report generated using create_processed_report()

Chromium 10x example

Data

For demonstrative purposes the data has been subsampled to 1GB.

The full experiment is available at: GSE111108

NN76_R1.fastq.gz

NN76_R2.fastq.gz

Aligned with Subread

R script for building index and downloading annotation

R script for processing

Aligned with STAR

R script for building index and downloading annotation

R script for processing

Example Report

Report generated using create_processed_report()

The scripts should be run in the order provided, and in the same folder as the data files. If an index and/or annotation already exists then the build-index.R script can be skipped and the processing script should be editted with the correct paths.

The workflows take around 1 hour to run on a 2016 Macbook Pro 15 with quad-core CPU.

Example Analysis

Mouse Blood Cells

Upstream data comes from CEL-seq2 example.

Analysis RMarkdown Report

Human Cell Atlas Spleen

Rscript for processing

Analysis RMarkdown Report