## Pipeline publication

[…] that the topology of coactivation networks of each cell changes as the olfactory sensory neuron cells mature. This work enables discovery of biologically meaningful genes through combined analysis of coactivation with genes known to be related to neuron maturity., A set of nine single cell RNA-Seq datasets were curated (Table ), all measuring transcriptomes of various neuronal cell populations in mice, with varying numbers of cells, sequencing strategies, and overall read depths. Raw sequencing reads were downloaded from the Gene Expression Omnibus (GEO), the Sequence Read Archive (SRA) or the European Nucleotide Archive (ENA). Fastq files were each mapped to the mm10 reference genome using STAR RNA-Seq aligner [] with default parameters. The resulting mapped read files were then converted to bam, sorted and indexed using Samtools [], and read counts for a total of 38806 genes were obtained using HTSeq-count [] under the mode ‘union’ with other default parameters. Read counts for multiple runs belonging to the same cell were added together, resulting in a raw count matrix for 38806 genes and 6377 cells. The data matrix was further transformed by calculating counts per million mapped reads (CPM) and taking the shifted log (log2CPM), i.e. \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$y_{ij} = \log _{2}(1 + 10^{6} r_{ij}/\sum _{k}r_{kj})$\end{document}yij=log2(1+106rij […]

library_books

### Integrated single cell data analysis reveals cell specific networks and novel coactivation markers

2016
PMCID: 5249008
PMID: 28105940
DOI: 10.1186/s12918-016-0370-4
Fundings: Australian Research Council, National Institutes of Health

## Pipeline specifications

 Software tools STAR, SAMtools, HTSeq