Commit d2196205 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

correct URL and DOI

parent f541955c

CITATION.cff

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@@ -11,7 +11,7 @@ authors: 
  email: "kai.battenberg@riken.jp"

  affiliation: "Center for Sustainable Resource Science, RIKEN, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Japan"

  orcid: "http://orcid.org/0000-0001-7517-2657"

version: 1.2.1

version: 1.2.3

doi: 10.1101/2021.01.19.427209

date-released: 2021-02-14

url: "https://github.com/minoda-lab/universc"

README.Rmd

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@@ -353,7 +353,7 @@ as follows: 


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: [https://doi.org/10.11.2.3021.01.19.427209](https://doi.org/10.11.2.3021.01.19.427209)

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 1.2.3. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)



```
@@ -362,7 +362,7 @@ package version 1.2.3. [https://github.com/minoda-lab/universc](https://github.c 
        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},

        elocation-id = {2021.01.19.427209},

        year = {2021},

        doi = {10.11.2.3021.01.19.427209},

        doi = {10.1101/2021.01.19.427209},

        publisher = {Cold Spring Harbor Laboratory},

        abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},

        eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},
@@ -1241,8 +1241,8 @@ bash /universc/launch_universc.sh --id "test-10x-v3" --technology "10x" \ 
Obtain DropSeq data from public database:



```

wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1.2.392\&format\=file\&file\=GSM1.2.392%5FPure%5FHumanMouse%2Ebam

mv index.html\?acc=GSM1.2.392\&format=file\&file=GSM1.2.392%5FPure%5FHumanMouse%2Ebam GSM1.2.39.bam

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 GSM1.2.39.bam

samtools sort -n GSM1.2.39.bam > GSM1.2.39.qsort

samtools view  GSM1.2.39.qsort  HUMAN_21:9825832-48085036 > GSM1.2.39.qsort2

samtools sort -O BAM GSM1.2.39.bam > GSM1.2.39.sort.bam
@@ -1250,17 +1250,17 @@ samtools index GSM1.2.39.sort.bam 
samtools view  GSM1.2.39.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.39.chr21.bam

samtools view -O BAM  GSM1.2.39.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.39.chr21.sort.bam

samtools sort -n GSM1.2.39.chr21.sort.bam -o GSM1.2.39.chr21.qsort.bam

bedtools bamtofastq -i GSM1.2.39.chr21.qsort.bam -fq GSM1.2.392_chr21_R1.fastq

mv GSM1.2.392_chr21_R1.fastq GSM1.2.392_chr21_R2.fastq

bedtools bamtofastq -i GSM1.2.39.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 GSM1.2.392_chr21_R2.fastq SRR1873277_1.fastq

fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq

head -n 117060 SRR1873277_1.fastq.paired.fq 117060 > SRR1873277_1.fastq.paired.fq

head -n 117060 GSM1.2.392_chr21_R2.fastq.paired.fq > GSM1.2.392_chr21_R2.fastq.paired.fq

cp SRR1873277_1.fastq.paired.fq  GSM1.2.392_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test

cp SRR1873277_1.fastq.paired.fq  GSM1.2.392_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test

head -n 117060 GSM1629193_chr21_R2.fastq.paired.fq > GSM1629193_chr21_R2.fastq.paired.fq

cp SRR1873277_1.fastq.paired.fq  GSM1629193_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test

cp SRR1873277_1.fastq.paired.fq  GSM1629193_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test

mv SRR1873277_1.fastq.paired.fq SRR1873277_R1.fastq

mv GSM1.2.392_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq

mv GSM1.2.392_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq

mv GSM1629193_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq

mv GSM1629193_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq

```



Run UniverSC:

README.html

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@@ -163,13 +163,13 @@ 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>A submission to a journal and biorXiv is in progress. Please cite these when they are available. Currently, the package can be cited as follows:</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/10.11.2.3021.01.19.427209" class="uri">https://doi.org/10.11.2.3021.01.19.427209</a> package version 1.2.3. <a href="https://github.com/minoda-lab/universc" class="uri">https://github.com/minoda-lab/universc</a></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" class="uri">https://doi.org/10.1101/2021.01.19.427209</a> package version 1.2.3. <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},

        elocation-id = {2021.01.19.427209},

        year = {2021},

        doi = {10.11.2.3021.01.19.427209},

        doi = {10.1101/2021.01.19.427209},

        publisher = {Cold Spring Harbor Laboratory},

        abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},

        eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},
@@ -649,8 +649,8 @@ bash /universc/launch_universc.sh --id &quot;test-10x-v3&quot; --technology &quo 
 &quot;/universc/test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002&quot;</code></pre>

<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\=GSM1.2.392\&amp;format\=file\&amp;file\=GSM1.2.392%5FPure%5FHumanMouse%2Ebam

mv index.html\?acc=GSM1.2.392\&amp;format=file\&amp;file=GSM1.2.392%5FPure%5FHumanMouse%2Ebam GSM1.2.39.bam

<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 GSM1.2.39.bam

samtools sort -n GSM1.2.39.bam &gt; GSM1.2.39.qsort

samtools view  GSM1.2.39.qsort  HUMAN_21:9825832-48085036 &gt; GSM1.2.39.qsort2

samtools sort -O BAM GSM1.2.39.bam &gt; GSM1.2.39.sort.bam
@@ -658,17 +658,17 @@ samtools index GSM1.2.39.sort.bam 
samtools view  GSM1.2.39.sort.bam  HUMAN_21:9825832-48085036 &gt; GSM1.2.39.chr21.bam

samtools view -O BAM  GSM1.2.39.sort.bam  HUMAN_21:9825832-48085036 &gt; GSM1.2.39.chr21.sort.bam

samtools sort -n GSM1.2.39.chr21.sort.bam -o GSM1.2.39.chr21.qsort.bam

bedtools bamtofastq -i GSM1.2.39.chr21.qsort.bam -fq GSM1.2.392_chr21_R1.fastq

mv GSM1.2.392_chr21_R1.fastq GSM1.2.392_chr21_R2.fastq

bedtools bamtofastq -i GSM1.2.39.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 GSM1.2.392_chr21_R2.fastq SRR1873277_1.fastq

fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq

head -n 117060 SRR1873277_1.fastq.paired.fq 117060 &gt; SRR1873277_1.fastq.paired.fq

head -n 117060 GSM1.2.392_chr21_R2.fastq.paired.fq &gt; GSM1.2.392_chr21_R2.fastq.paired.fq

cp SRR1873277_1.fastq.paired.fq  GSM1.2.392_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test

cp SRR1873277_1.fastq.paired.fq  GSM1.2.392_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test

head -n 117060 GSM1629193_chr21_R2.fastq.paired.fq &gt; GSM1629193_chr21_R2.fastq.paired.fq

cp SRR1873277_1.fastq.paired.fq  GSM1629193_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test

cp SRR1873277_1.fastq.paired.fq  GSM1629193_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test

mv SRR1873277_1.fastq.paired.fq SRR1873277_R1.fastq

mv GSM1.2.392_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq

mv GSM1.2.392_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq</code></pre>

mv GSM1629193_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq

mv GSM1629193_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq</code></pre>

<p>Run UniverSC:</p>

<pre><code>bash universc/launch_universc.sh -t &quot;DropSeq&quot; --setup

# call on dropseq with files

README.md

+12 −12
Original line number Diff line number Diff line
@@ -353,7 +353,7 @@ as follows: 


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: [https://doi.org/10.11.2.3021.01.19.427209](https://doi.org/10.11.2.3021.01.19.427209)

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 1.2.3. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)



```
@@ -362,7 +362,7 @@ package version 1.2.3. [https://github.com/minoda-lab/universc](https://github.c 
        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},

        elocation-id = {2021.01.19.427209},

        year = {2021},

        doi = {10.11.2.3021.01.19.427209},

        doi = {10.1101/2021.01.19.427209},

        publisher = {Cold Spring Harbor Laboratory},

        abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},

        eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},
@@ -1241,8 +1241,8 @@ bash /universc/launch_universc.sh --id "test-10x-v3" --technology "10x" \ 
Obtain DropSeq data from public database:



```

wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1.2.392\&format\=file\&file\=GSM1.2.392%5FPure%5FHumanMouse%2Ebam

mv index.html\?acc=GSM1.2.392\&format=file\&file=GSM1.2.392%5FPure%5FHumanMouse%2Ebam GSM1.2.39.bam

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 GSM1.2.39.bam

samtools sort -n GSM1.2.39.bam > GSM1.2.39.qsort

samtools view  GSM1.2.39.qsort  HUMAN_21:9825832-48085036 > GSM1.2.39.qsort2

samtools sort -O BAM GSM1.2.39.bam > GSM1.2.39.sort.bam
@@ -1250,17 +1250,17 @@ samtools index GSM1.2.39.sort.bam 
samtools view  GSM1.2.39.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.39.chr21.bam

samtools view -O BAM  GSM1.2.39.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.39.chr21.sort.bam

samtools sort -n GSM1.2.39.chr21.sort.bam -o GSM1.2.39.chr21.qsort.bam

bedtools bamtofastq -i GSM1.2.39.chr21.qsort.bam -fq GSM1.2.392_chr21_R1.fastq

mv GSM1.2.392_chr21_R1.fastq GSM1.2.392_chr21_R2.fastq

bedtools bamtofastq -i GSM1.2.39.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 GSM1.2.392_chr21_R2.fastq SRR1873277_1.fastq

fastq_pair GSM1629193_chr21_R2.fastq SRR1873277_1.fastq

head -n 117060 SRR1873277_1.fastq.paired.fq 117060 > SRR1873277_1.fastq.paired.fq

head -n 117060 GSM1.2.392_chr21_R2.fastq.paired.fq > GSM1.2.392_chr21_R2.fastq.paired.fq

cp SRR1873277_1.fastq.paired.fq  GSM1.2.392_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test

cp SRR1873277_1.fastq.paired.fq  GSM1.2.392_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test

head -n 117060 GSM1629193_chr21_R2.fastq.paired.fq > GSM1629193_chr21_R2.fastq.paired.fq

cp SRR1873277_1.fastq.paired.fq  GSM1629193_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test

cp SRR1873277_1.fastq.paired.fq  GSM1629193_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test

mv SRR1873277_1.fastq.paired.fq SRR1873277_R1.fastq

mv GSM1.2.392_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq

mv GSM1.2.392_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq

mv GSM1629193_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq

mv GSM1629193_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq

```



Run UniverSC:

inst/CITATION

+2 −2
Original line number Diff line number Diff line
@@ -6,7 +6,7 @@ as follows: 


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: [https://doi.org/10.11.2.3021.01.19.427209](https://doi.org/10.11.2.3021.01.19.427209)

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 1.2.3. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)



```
@@ -15,7 +15,7 @@ package version 1.2.3. [https://github.com/minoda-lab/universc](https://github.c 
        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},

        elocation-id = {2021.01.19.427209},

        year = {2021},

        doi = {10.11.2.3021.01.19.427209},

        doi = {10.1101/2021.01.19.427209},

        publisher = {Cold Spring Harbor Laboratory},

        abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},

        eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},

CRA Git | Maintained and supported by SUSTech CRA and CCSE