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restore paths in documentation
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@TomKellyGenetics
TomKellyGenetics committed Feb 14, 2022
1 parent 8b22075 commit bd0bcc9
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10 changes: 5 additions & 5 deletions README.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -939,14 +939,14 @@ cellrangerpath=`which cellranger`
if [[ ! -f test/cellranger_reference/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 test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA
fi
if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.1/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.1/star/SA ]]; then
rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.1/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.1/star/SA
if [[ ! -f test/cellranger_reference/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 test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA
fi
```

This creates a reference for Cell Ranger here:

- test/cellranger_reference/cellranger-tiny-ref/1.2.1
- test/cellranger_reference/cellranger-tiny-ref/1.2.0

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

Expand Down Expand Up @@ -985,13 +985,13 @@ gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.1.gff3 -T -o tes
To generate new references we first remove the references imported.

```
rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.1 test/cellranger_reference/cellranger-tiny-ref/3.0.0
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/1.2.1 \
cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/1.2.0 \
--fasta=test/cellranger_reference/cellranger-tiny-ref/genome-1.2.1.fa \
--genes=test/cellranger_reference/cellranger-tiny-ref/ genes-1.2.1.gtf
Expand Down
10 changes: 5 additions & 5 deletions README.html
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Original file line number Diff line number Diff line change
Expand Up @@ -435,12 +435,12 @@ <h3 id="setting-up-cell-ranger-references">Setting up Cell Ranger references</h3
if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] &amp;&amp; [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then
rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA
fi
if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.1/star/SA ]] &amp;&amp; [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.1/star/SA ]]; then
rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.1/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.1/star/SA
if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] &amp;&amp; [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then
rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA
fi</code></pre>
<p>This creates a reference for Cell Ranger here:</p>
<ul>
<li><p>test/cellranger_reference/cellranger-tiny-ref/1.2.1</p></li>
<li><p>test/cellranger_reference/cellranger-tiny-ref/1.2.0</p></li>
<li><p>test/cellranger_reference/cellranger-tiny-ref/3.0.0</p></li>
</ul>
<h4 id="automated-references">Automated references</h4>
Expand All @@ -457,9 +457,9 @@ <h4 id="custom-cell-ranger-references">Custom Cell Ranger references</h4>
<p>The <code>gffread</code> function includes with the <a href="http://cole-trapnell-lab.github.io/cufflinks/file_formats/#the-gffread-utility">cufflinks</a> utility can convert to gtf. For example:</p>
<pre><code>gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.1.gff3 -T -o test/cellranger_reference/cellranger-tiny-ref/genes-1.2.1.gtf </code></pre>
<p>To generate new references we first remove the references imported.</p>
<pre><code>rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.1 test/cellranger_reference/cellranger-tiny-ref/3.0.0</code></pre>
<pre><code>rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0</code></pre>
<p>We then generate references from the FASTA and GTF files as shown in the following examples:</p>
<pre><code>cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/1.2.1 \
<pre><code>cellranger mkref --genome=test/cellranger_reference/cellranger-tiny-ref/1.2.0 \
--fasta=test/cellranger_reference/cellranger-tiny-ref/genome-1.2.1.fa \
--genes=test/cellranger_reference/cellranger-tiny-ref/ genes-1.2.1.gtf

Expand Down
14 changes: 7 additions & 7 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -939,14 +939,14 @@ cellrangerpath=`which cellranger`
if [[ ! -f test/cellranger_reference/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 test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA
fi
if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.1/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.1/star/SA ]]; then
rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.1/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.1/star/SA
if [[ ! -f test/cellranger_reference/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 test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA
fi
```

This creates a reference for Cell Ranger here:

- test/cellranger_reference/cellranger-tiny-ref/1.2.1
- test/cellranger_reference/cellranger-tiny-ref/1.2.0

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

Expand Down Expand Up @@ -985,15 +985,15 @@ gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.1.gff3 -T -o tes
To generate new references we first remove the references imported.

```
rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.1 test/cellranger_reference/cellranger-tiny-ref/3.0.0
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/1.2.1 \
--fasta=test/cellranger_reference/cellranger-tiny-ref/genome-1.2.1.fa \
--genes=test/cellranger_reference/cellranger-tiny-ref/ genes-1.2.1.gtf
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 \
Expand Down

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