Merge branch 'master' of dgt-gitlab.gsc.riken.jp:tom/cellranger_convert

---

title: "UniverSC: Single-cell processing across technologies"

author: "S. Thomas Kelly^1†^, Kai Battenberg^1,2†^, Makoto Hayashi^2^, Aki Minoda^1^ <br> ^1^ RIKEN Center for Integrative Medical Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama <br> ^2^ RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama <br> † These authors contributed equally to this work"

affiliations:

 - name: "RIKEN Center for Integrative Medical Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan"

   index: 1

 - name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan"

   index: 2

date: "Thursday 09 July 2020"

output:

  prettydoc::html_pretty:

       theme: cayman

       number_sections: true

       toc: true

       toc_depth: 4

       keep_md: true

       keep_html: true

toc-title: "Table of Contents"

tags:

  - single-cell

  - next-generation-sequencing

  - UMI-tools

  - genomics

  - gene-expression

  - scRNA-Seq

  - bioinformatics

  - data-processing

---

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### UniverSC version 1.0.0

# UniverSC

#### Single-cell processing across technologies

**Single-cell processing across technologies**

------------------------------------------

Provides a conversion script to run multiple technologies and custom libraries with cellranger (10x Genomics analysis tool).

**Summary**

Guide on how to simulate gene expression data from pathway structures defined by graphs from `igraph` objects.

**Package**

UniverSC version 1.0.0

**Maintainers**

Tom Kelly^†^ (RIKEN IMS) and Kai Battenberg^†^ (RIKEN CSRS/IMS)

† These authors contributed equally to this work

Contact: <first name>.<family name>[at]riken.jp

------------------------------------------

## Getting Started

### Advanced users

If you have `cellranger` already installed, then all you need to do is clone or download this git repository. You can then run the script in this directory or add it your `PATH`. See the [Quick Start](#quick-start) guide below.

If you wish to install `cellranger` and configure this script to run on a Linux environment, we provide details on [installation](#installation) below. Note that `launch_universc.sh` requires write-access a cellranger installation so it needs to be installed in a user's "home" directory on a server. No admin powers needed!

Note that `cellranger` installations that are pre-compiled on Linux will not run on Mac or Windows. Note that Mac OS and some Linux distributions also have different version of sed and rename. It is possible to compile an open-source version of cellranger but it is tricky to install the dependencies so we recommend using our docker [image](#Docker) if you wish to do this. 

### Beginners

If you are a beginner bioinformatician or wish to run this on a local computer (Mac or Windows), no problem! We provide a "docker" image containing everything needed to run it without installing the software needed. All you need to do is install [docker](https://docs.docker.com/desktop/) and follow our guide to use the [image](#Docker). This comes bundled with all the compatible versions needed to run it.

Note that you need to run the shell commands given in a unix-like command-line interface (the "Terminal" application on Mac or Linux systems). Many shells are supported but we recommend the "bash" shell for beginners (this is the default on most systems). Windows 10 includes a [subsystem](https://docs.microsoft.com/en-us/windows/wsl/install-win10) to run `bash`. If this is too complicated, you can open a Linux environment (Ubuntu) in docker by following our instructions. Then you can enter bash commands into the terminal opened by docker.

If you run into problems installing or running `launch_universc.sh` please don't hesistate to contact us via email or GitHub.

##### Tom Kelly (RIKEN IMS) and Kai Battenberg (RIKEN CSRS/IMS)

## Purpose

new features to the maintainers with and [issue](#Issues) on GitHub. Details on how to [install](#Install) and [run](#Usage) are provided

below. Please see the [help](#Help) and [examples](#Examples) to try solve your problem before submitting an issue.

Details on the [Docker image](#Docker) are given below.

Details on the [Docker image](#Docker) are given below. We recommend using Docker unless you have a server environment with cellranger installed already.

### Supported Technologies

-  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq

-  ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

- inDrops

    -  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

    -  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

    -  inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1

    -  inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2

    -  inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

-  Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384

-  Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536

#### Custom inputs

Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"

Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by a "_" character.

 e.g. Custom (16bp barcode, 10bp UMI): custom_16_10

 e.g. Custom (16bp barcode, 10bp UMI): `custom_16_10`

Custom barcode files are also supported for preset technologies. These are particularly useful for well-based

technologies to demutliplex based on the wells.

## Release

This tool will be released open-source. We welcome any feedback on it.

This tool will be released open-source (see [legal stuff](#licensing) below).

We welcome any feedback on it and any contributions to improve it.

Hopefully it will save people time by making it easier to compare technologies.

We have tested it on several technologies but we need users like you

- make 3.81

- git 2.20.1 

- sed (GNU sed) 4.4

- sed (GNU sed) 4.4 (gsed)

- tar  2.8.3

- rename 0.20 (perl-rename)

- perl 5.26.1

sudo dnf install prename

```

Ret Hat Linux:

Red Hat Linux:

```

sudo rpm install prename

                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

                                  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq

                                  ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

                                  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

                                  inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2

                                  inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

                                  Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384

                                  Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536

- add example running on custom barcode whitelist

### Licensing

## Licensing

This package is provided open-source on a GPL-3 license. This means that you are free to use and 

modify this code provided that they also contain this license.