Commit 8bb9bb43 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update documentation for 1.2.1

parent 4e4a0317

README.Rmd

+5 −5
Original line number Diff line number Diff line
@@ -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/1.2.0/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

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

fi

```



This creates a reference for Cell Ranger here:



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

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



- test/cellranger_reference/cellranger-tiny-ref/3.0.0
@@ -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/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.1 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 \

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

README.html

+5 −5
Original line number Diff line number Diff line
@@ -435,12 +435,12 @@ 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/1.2.0/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

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

fi</code></pre>

<p>This creates a reference for Cell Ranger here:</p>

<ul>

<li><p>test/cellranger_reference/cellranger-tiny-ref/1.2.0</p></li>

<li><p>test/cellranger_reference/cellranger-tiny-ref/1.2.1</p></li>

<li><p>test/cellranger_reference/cellranger-tiny-ref/3.0.0</p></li>

</ul>

<h4 id="automated-references">Automated references</h4>
@@ -457,9 +457,9 @@ cd ../../..</code></pre> 
<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/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0</code></pre>

<pre><code>rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.1 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/1.2.0 \

<pre><code>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

README.md

+5 −5
Original line number Diff line number Diff line
@@ -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/1.2.0/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

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

fi

```



This creates a reference for Cell Ranger here:



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

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



- test/cellranger_reference/cellranger-tiny-ref/3.0.0
@@ -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/1.2.0 test/cellranger_reference/cellranger-tiny-ref/3.0.0

rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.1 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 \

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

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