Commit 02f48685 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

correct versions in documentation

parent ef920957

README.Rmd

+9 −9
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@@ -1276,15 +1276,15 @@ Obtain DropSeq data from public database: 


```

wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629193\&format\=file\&file\=GSM1629193%5FPure%5FHumanMouse%2Ebam

mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1.2.49.bam

samtools sort -n GSM1.2.49.bam > GSM1.2.49.qsort

samtools view  GSM1.2.49.qsort  HUMAN_21:9825832-48085036 > GSM1.2.49.qsort2

samtools sort -O BAM GSM1.2.49.bam > GSM1.2.49.sort.bam

samtools index GSM1.2.49.sort.bam

samtools view  GSM1.2.49.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.49.chr21.bam

samtools view -O BAM  GSM1.2.49.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.49.chr21.sort.bam

samtools sort -n GSM1.2.49.chr21.sort.bam -o GSM1.2.49.chr21.qsort.bam

bedtools bamtofastq -i GSM1.2.49.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq

mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1629192.bam

samtools sort -n GSM1629192.bam > GSM1629192.qsort

samtools view  GSM1629192.qsort  HUMAN_21:9825832-48085036 > GSM1629192.qsort2

samtools sort -O BAM GSM1629192.bam > GSM1629192.sort.bam

samtools index GSM1629192.sort.bam

samtools view  GSM1629192.sort.bam  HUMAN_21:9825832-48085036 > GSM1629192.chr21.bam

samtools view -O BAM  GSM1629192.sort.bam  HUMAN_21:9825832-48085036 > GSM1629192.chr21.sort.bam

samtools sort -n GSM1629192.chr21.sort.bam -o GSM1629192.chr21.qsort.bam

bedtools bamtofastq -i GSM1629192.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq

mv GSM1629193_chr21_R1.fastq GSM1629193_chr21_R2.fastq

fastq-dump -F --split-files SRR1873277

fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq

README.html

+13 −13
Original line number Diff line number Diff line 
<p><img src="https://img.shields.io/docker/automated/tomkellygenetics/universc?label=docker%20local%20build" alt="Docker Manual build" /> <img src="https://img.shields.io/docker/cloud/automated/tomkellygenetics/universc?label=docker%20cloud%20build" alt="Docker Cloud Build" /> <img src="https://img.shields.io/docker/cloud/build/tomkellygenetics/universc?label=cloud%20build" alt="Docker Cloud Status" /> <img src="https://img.shields.io/docker/stars/tomkellygenetics/universc" alt="Docker Stars" /> <img src="https://img.shields.io/docker/pulls/tomkellygenetics/universc" alt="Docker Pulls" /></p>

<p><img src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.4" alt="Docker Image Version (tag latest semver)" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%22layers@1.2.4%22" alt="MicroBadger Layers (latest)" /> <img src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.4?label=%22image%20size@1.2.4" alt="Docker Image Size (v1.2.4)" /> <img src="https://img.shields.io/docker/v/tomkellygenetics/universc/latest" alt="Docker Image Version (latest by date)" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest" alt="MicroBadger Layers (latest)" /> <img src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/latest" alt="Docker Image Size (latest)" /></p>

<p><embed src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.4" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%22layers@1.2.4%22" alt="MicroBadger Layers (latest)" /> <embed src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.4?label=%22image%20size@1.2.4" /> <img src="https://img.shields.io/docker/v/tomkellygenetics/universc/latest" alt="Docker Image Version (latest by date)" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest" alt="MicroBadger Layers (latest)" /> <img src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/latest" alt="Docker Image Size (latest)" /></p>

<p><img src="https://img.shields.io/github/checks-status/minoda-lab/universc/master?label=GitHub%20checks" alt="GitHub branch checks state" /> <img src="https://img.shields.io/github/release-date/minoda-lab/universc" alt="GitHub Release Date" /> <img src="https://img.shields.io/github/last-commit/minoda-lab/universc/master" alt="GitHub last commit (branch)" /> <img src="https://img.shields.io/github/issues/minoda-lab/universc" alt="GitHub issues" /> <img src="https://img.shields.io/github/issues-pr/minoda-lab/universc" alt="GitHub pull requests" /></p>

<p><a href="http://hits.dwyl.com/minoda-lab/universc"><img src="http://hits.dwyl.com/minoda-lab/universc.svg" alt="GitHub Views" /></a> <a href="http://hits.dwyl.com/tomkellygenetics/universc"><img src="http://hits.dwyl.com/tomkellygenetics/universc.svg" alt="GitHub Views" /></a> <img src="https://img.shields.io/github/search/minoda-lab/universc/master" alt="GitHub search hit counter" /> <img src="https://img.shields.io/github/forks/minoda-lab/universc?style=social" alt="GitHub forks" /> <img src="https://img.shields.io/github/stars/minoda-lab/universc?style=social" alt="GitHub Repo stars" /> <img src="https://img.shields.io/github/watchers/minoda-lab/universc?style=social" alt="GitHub watchers" /></p>

<p><img src="https://img.shields.io/github/languages/code-size/minoda-lab/universc" alt="GitHub code size in bytes" /> <img src="https://img.shields.io/github/repo-size/minoda-lab/universc" alt="GitHub repo size" /> <img src="https://img.shields.io/github/languages/top/minoda-lab/universc" alt="GitHub top language" /> <img src="https://img.shields.io/github/languages/count/minoda-lab/universc" alt="GitHub language count" /> <a href="https://doi.org/10.5281/zenodo.7116956"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.7116956.svg" alt="Zenodo DOI" /></a></p>
@@ -169,7 +169,7 @@ cat Sample1_I2_file.fastq.gz Sample2_I2_file.fastq.gz Sample3_I2_file.fastq.gz & 
<p>We have tested it on several technologies but we need users like you to let us know how we can improve it. We hope that it will save you time by handing tedious parts of data formatting so that you can focus on the results.</p>

<h3 id="citation">Citation <span id="Citation"><span></h3>

<p>Please cite our publication when you use our software as follows:</p>

<p>Battenberg, K., Kelly, S.T., Ras, R.A., Hetherington, N.A., Hayashi, K., and Minoda, A. (2022) A flexible cross-platform single-cell data processing pipeline. <e>Nat Commun</e> <b>13</b>(1): 1-7. https://doi.org/10.1038/s41467-022-34681-z</p>

<p>Battenberg, K., Kelly, S.T., Ras, R.A., Hetherington, N.A., Hayashi, K., and Minoda, A. (2022) A flexible cross-platform single-cell data processing pipeline. <em>Nat Commun</em> <strong>13</strong>(1): 1-7. https://doi.org/10.1038/s41467-022-34681-z</p>

<pre><code>@Article{pmid36369450,

        author=&quot;Battenberg, K.  and Kelly, S. T.  and Ras, R. A.  and Hetherington, N. A.  and Hayashi, M.  and Minoda, A. &quot;,

        title=&quot;{{A} flexible cross-platform single-cell data processing pipeline}&quot;,
@@ -183,7 +183,7 @@ cat Sample1_I2_file.fastq.gz Sample2_I2_file.fastq.gz Sample3_I2_file.fastq.gz & 
        URL = {https://doi.org/10.1038/s41467-022-34681-z}

}</code></pre>

<p>The preprint can also be found here:</p>

<p>Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021) UniverSC: a flexible cross-platform single-cell data processing pipeline. bioRxiv 2021.01.19.427209; doi: <a href="https://doi.org/10.1101/2021.01.19.427209">https://doi.org/10.1101/2021.01.19.427209</a> package version 1.2.4. <a href="https://github.com/minoda-lab/universc">https://github.com/minoda-lab/universc</a></p>

<p>Kelly, S.T., Battenberg K., Hetherington, N.A., Hayashi, K., and Minoda, A. (2021) UniverSC: a flexible cross-platform single-cell data processing pipeline. bioRxiv 2021.01.19.427209; doi: <a href="https://doi.org/10.1101/2021.01.19.427209" class="uri">https://doi.org/10.1101/2021.01.19.427209</a> package version 1.2.4. <a href="https://github.com/minoda-lab/universc" class="uri">https://github.com/minoda-lab/universc</a></p>

<pre><code>@article {Kelly2021.01.19.427209,

        author = {Kelly, S. Thomas and Battenberg, Kai and Hetherington, Nicola A. and Hayashi, Makoto and Minoda, Aki},

        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},
@@ -425,7 +425,7 @@ docker run hello-world </code></pre> 
<pre><code>docker run -it tomkellygenetics/universc:latest /bin/zsh </code></pre>

<p>Either of these shells are supported.</p>

<p>Note that Docker containers run with a default of 2 GB of memory. It is recommended to use at least 8 GB of memory as this is often insufficient for running UniverSC. Ideally, 16 GB of memory should be used if it is available on your system.</p>

<pre><code>docker run --memory 16g -it tomkellygenetics/universc:latest /bin/bash</code></pre>

<p><code>docker run --memory 16g -it tomkellygenetics/universc:latest /bin/bash</code></p>

<h5 id="building-the-docker-image-locally">Building the Docker image locally</h5>

<p>The Dockerfile is provided in the repository so it can be built from source. This will build a Docker image with the latest version of universc provided that updates to dependencies on GitHub are still compatible.</p>

<pre><code>git clone https://github.com/minoda-lab/universc.git
@@ -671,15 +671,15 @@ bash /universc/launch_universc.sh --id &quot;test-10x-v3&quot; --technology &quo 
<h4 id="running-launch_universc.sh-on-dropseq-data">Running launch_universc.sh on DropSeq data</h4>

<p>Obtain DropSeq data from public database:</p>

<pre><code>wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629193\&amp;format\=file\&amp;file\=GSM1629193%5FPure%5FHumanMouse%2Ebam

mv index.html\?acc=GSM1629193\&amp;format=file\&amp;file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1.2.49.bam

samtools sort -n GSM1.2.49.bam &gt; GSM1.2.49.qsort

samtools view  GSM1.2.49.qsort  HUMAN_21:9825832-48085036 &gt; GSM1.2.49.qsort2

samtools sort -O BAM GSM1.2.49.bam &gt; GSM1.2.49.sort.bam

samtools index GSM1.2.49.sort.bam

samtools view  GSM1.2.49.sort.bam  HUMAN_21:9825832-48085036 &gt; GSM1.2.49.chr21.bam

samtools view -O BAM  GSM1.2.49.sort.bam  HUMAN_21:9825832-48085036 &gt; GSM1.2.49.chr21.sort.bam

samtools sort -n GSM1.2.49.chr21.sort.bam -o GSM1.2.49.chr21.qsort.bam

bedtools bamtofastq -i GSM1.2.49.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq

mv index.html\?acc=GSM1629193\&amp;format=file\&amp;file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1629192.bam

samtools sort -n GSM1629192.bam &gt; GSM1629192.qsort

samtools view  GSM1629192.qsort  HUMAN_21:9825832-48085036 &gt; GSM1629192.qsort2

samtools sort -O BAM GSM1629192.bam &gt; GSM1629192.sort.bam

samtools index GSM1629192.sort.bam

samtools view  GSM1629192.sort.bam  HUMAN_21:9825832-48085036 &gt; GSM1629192.chr21.bam

samtools view -O BAM  GSM1629192.sort.bam  HUMAN_21:9825832-48085036 &gt; GSM1629192.chr21.sort.bam

samtools sort -n GSM1629192.chr21.sort.bam -o GSM1629192.chr21.qsort.bam

bedtools bamtofastq -i GSM1629192.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq

mv GSM1629193_chr21_R1.fastq GSM1629193_chr21_R2.fastq

fastq-dump -F --split-files SRR1873277

fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq

README.md

+11 −11
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@@ -6,7 +6,7 @@ affiliations: 
   index: 1

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

   index: 2

date: "Monday 17 October 2022"

date: "Saturday 24 December 2022"

output:

  prettydoc::html_pretty:

       theme: cayman
@@ -382,7 +382,7 @@ A flexible cross-platform single-cell data processing pipeline. _Nat Commun_ **1 


The preprint can also be found here:



Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021)

Kelly, S.T., Battenberg K., Hetherington, N.A., Hayashi, K., and Minoda, A. (2021)

UniverSC: a flexible cross-platform single-cell data processing pipeline.

bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.1101/2021.01.19.427209](https://doi.org/10.1101/2021.01.19.427209)

package version 1.2.4. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
@@ -1276,15 +1276,15 @@ Obtain DropSeq data from public database: 


```

wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1629193\&format\=file\&file\=GSM1629193%5FPure%5FHumanMouse%2Ebam

mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1.2.49.bam

samtools sort -n GSM1.2.49.bam > GSM1.2.49.qsort

samtools view  GSM1.2.49.qsort  HUMAN_21:9825832-48085036 > GSM1.2.49.qsort2

samtools sort -O BAM GSM1.2.49.bam > GSM1.2.49.sort.bam

samtools index GSM1.2.49.sort.bam

samtools view  GSM1.2.49.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.49.chr21.bam

samtools view -O BAM  GSM1.2.49.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.49.chr21.sort.bam

samtools sort -n GSM1.2.49.chr21.sort.bam -o GSM1.2.49.chr21.qsort.bam

bedtools bamtofastq -i GSM1.2.49.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq

mv index.html\?acc=GSM1629193\&format=file\&file=GSM1629193%5FPure%5FHumanMouse%2Ebam GSM1629192.bam

samtools sort -n GSM1629192.bam > GSM1629192.qsort

samtools view  GSM1629192.qsort  HUMAN_21:9825832-48085036 > GSM1629192.qsort2

samtools sort -O BAM GSM1629192.bam > GSM1629192.sort.bam

samtools index GSM1629192.sort.bam

samtools view  GSM1629192.sort.bam  HUMAN_21:9825832-48085036 > GSM1629192.chr21.bam

samtools view -O BAM  GSM1629192.sort.bam  HUMAN_21:9825832-48085036 > GSM1629192.chr21.sort.bam

samtools sort -n GSM1629192.chr21.sort.bam -o GSM1629192.chr21.qsort.bam

bedtools bamtofastq -i GSM1629192.chr21.qsort.bam -fq GSM1629193_chr21_R1.fastq

mv GSM1629193_chr21_R1.fastq GSM1629193_chr21_R2.fastq

fastq-dump -F --split-files SRR1873277

fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq

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