add set up for references to manuals

export PATH=$HOME/Downloads/universc:$PATH

```

### Setting up Cell Ranger references

This repository comes with almost all necessary files to run test jobs. Test data and

Cell Ranger references are available with Git large file storage (LFS).

To install git LFS run:

```

curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | sudo bash

sudo apt-get install git-lfs

git lfs install

```

To import large files from Github change to the "universc" directory and run:

```

git lfs pull origin

```

This provides almost all files required. The STAR index and reference need to be generated or

imported from an existing reference. The following code detects whether the references are

available in an existing cellranger installation.

```

cd test

cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`

# set up cellranger reference

if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA

fi

cd ..

```

This creates a reference for Cell Ranger here:

- test/cellranger_reference/cellranger-tiny-ref/1.2.0

- test/cellranger_reference/cellranger-tiny-ref/3.0.0

#### Automated references

You can reset the references with the automated settings here:

```

cd test/cellranger_reference/cellranger-tiny-ref/

make clean

make reference

cd ../../..

```

#### Custom Cell Ranger references

It is also possible to generate a custom reference for any genome provided you have

a FASTQ genome reference file and a GTF/GFF3 annotation file. Please ensure that the

chromosomes match between the FASTA headers and the chromosome column (1st) of the

GTF/GFF3 file.

The `gffread` function includes with the [cufflinks](http://cole-trapnell-lab.github.io/cufflinks/file_formats/#the-gffread-utility)

utility can convert to gtf. For example:

```

gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.0.gff3 -T -o test/cellranger_reference/cellranger-tiny-ref/genes-1.2.0.gtf 

```

To generate new references we first remove the references imported.

```

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0

```

We then generate references from the FASTA and GTF files as shown in the following examples:

```

cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/1.2.0 \

        --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-1.2.0.fa \

        --genes=test/cellranger_reference/cellranger-tiny-ref/ genes-1.2.0.gtf

cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/3.0.0 \

         --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-3.0.0.fa \

         --genes=test/cellranger_reference/cellranger-tiny-ref/ genes-3.0.0.gtf

```

See the Cell Ranger manuals for more [details on references](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references). 

## Usage <span id="Usage"><span>

   index: 1

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

   index: 2

date: "Tuesday 08 December 2020"

date: "Wednesday 20 January 2021"

output:

  prettydoc::html_pretty:

       theme: cayman

export PATH=$HOME/Downloads/universc:$PATH

```

### Setting up Cell Ranger references

This repository comes with almost all necessary files to run test jobs. Test data and

Cell Ranger references are available with Git large file storage (LFS).

To install git LFS run:

```

curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | sudo bash

sudo apt-get install git-lfs

git lfs install

```

To import large files from Github change to the "universc" directory and run:

```

git lfs pull origin

```

This provides almost all files required. The STAR index and reference need to be generated or

imported from an existing reference. The following code detects whether the references are

available in an existing cellranger installation.

```

cd test

cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`

# set up cellranger reference

if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA /home/tom/local/bin/cellranger-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA

fi

cd ..

```

This creates a reference for Cell Ranger here:

- test/cellranger_reference/cellranger-tiny-ref/1.2.0

- test/cellranger_reference/cellranger-tiny-ref/3.0.0

#### Automated references

You can reset the references with the automated settings here:

```

cd test/cellranger_reference/cellranger-tiny-ref/

make clean

make reference

cd ../../..

```

#### Custom Cell Ranger references

It is also possible to generate a custom reference for any genome provided you have

a FASTQ genome reference file and a GTF/GFF3 annotation file. Please ensure that the

chromosomes match between the FASTA headers and the chromosome column (1st) of the

GTF/GFF3 file.

The `gffread` function includes with the [cufflinks](http://cole-trapnell-lab.github.io/cufflinks/file_formats/#the-gffread-utility)

utility can convert to gtf. For example:

```

gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.0.gff3 -T -o test/cellranger_reference/cellranger-tiny-ref/genes-1.2.0.gtf 

```

To generate new references we first remove the references imported.

```

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0

```

We then generate references from the FASTA and GTF files as shown in the following examples:

```

cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/1.2.0 \

        --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-1.2.0.fa \

        --genes=test/cellranger_reference/cellranger-tiny-ref/ genes-1.2.0.gtf

cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/3.0.0 \

         --fasta=test/cellranger_reference/cellranger-tiny-ref/genome-3.0.0.fa \

         --genes=test/cellranger_reference/cellranger-tiny-ref/ genes-3.0.0.gtf

```

See the Cell Ranger manuals for more [details on references](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references). 

## Usage <span id="Usage"><span>