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add PIP-Seq and VASA-Seq to documentation (work-in-progress)
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@TomKellyGenetics
TomKellyGenetics committed Sep 19, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG
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- updates STRT-Seq to default to passing (undocumented) SC5P-R1 chemistry inputs to Cell Ranger
- enables SC5P-R1 chemistry to run without read2 arguments
- adds custom parameters (STRT-Seq-2018 technology) for Fan et al., (2018) https://doi.org/10.1038/s41422-018-0053-3
- adds PIP-Seq parameters (work-in-progress)
- adds VASA-Seq parameters (work-in-progress)

# 1.2.6

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14 changes: 14 additions & 0 deletions README.Rmd
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Expand Up @@ -212,6 +212,11 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
- MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
- Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
- Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq
- PIP-Seq
- PIP-Seq version 1 (16 bp barcode, 6 bp UMI): pip-seq-v1
- PIP-Seq version 2 (24 bp barcode, 12 bp UMI): pip-seq-v2
- PIP-Seq version 3 (28 bp barcode, 12 bp UMI): pip-seq-v3
- PIP-Seq version 4 (28 bp barcode, 12 bp UMI): pip-seq-v4
- Quartz-Seq
- QuartzSeq (6 bp index, no UMI): quartz-seq
- Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
Expand All @@ -236,6 +241,9 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
- STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i
- STRT-Seq-2018 (8 bp barcode, 8 bp UMI): strt-seq-2018
- SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad
- VASA-Seq
- VASA-plate (6 bp UMI, 6 bp barcode): vasa-plate
- VASA-drop (6 bp UMI, 16 bp barcode): vasa-drop

#### Chemistry settings available

Expand Down Expand Up @@ -1192,6 +1200,10 @@ Mandatory arguments to long options are mandatory for short options too.
MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1
MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
PIP-Seq version 1 (16 bp barcode, 6 bp UMI): pip-seq-v1
PIP-Seq version 2 (24 bp barcode, 12 bp UMI): pip-seq-v2
PIP-Seq version 3 (28 bp barcode, 12 bp UMI): pip-seq-v3, fluent-bio-v3
PIP-Seq version 4 (28 bp barcode, 12 bp UMI): pip-seq-v4, fluent-bio-v4
QuartzSeq (6 bp index, no UMI): quartz-seq
Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536
Expand All @@ -1211,6 +1223,8 @@ Mandatory arguments to long options are mandatory for short options too.
STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i
STRT-Seq-2018 (8 bp barcode, 8 bp UMI): strt-seq-2018
SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad
VASA-plate (6 bp UMI, 6 bp barcode): vasa-plate
VASA-drop (6 bp UMI, 16 bp barcode): vasa-drop
Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10
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21 changes: 20 additions & 1 deletion README.html
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Expand Up @@ -277,6 +277,13 @@ <h4 id="pre-set-configurations">Pre-set configurations</h4>
</ul></li>
<li>Microwell-Seq (18 bp barcode, 6 bp UMI): microwell</li>
<li>Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq</li>
<li>PIP-Seq
<ul>
<li>PIP-Seq version 1 (16 bp barcode, 6 bp UMI): pip-seq-v1</li>
<li>PIP-Seq version 2 (24 bp barcode, 12 bp UMI): pip-seq-v2</li>
<li>PIP-Seq version 3 (28 bp barcode, 12 bp UMI): pip-seq-v3</li>
<li>PIP-Seq version 4 (28 bp barcode, 12 bp UMI): pip-seq-v4</li>
</ul></li>
<li>Quartz-Seq
<ul>
<li>QuartzSeq (6 bp index, no UMI): quartz-seq</li>
Expand Down Expand Up @@ -308,9 +315,15 @@ <h4 id="pre-set-configurations">Pre-set configurations</h4>
<li>STRT-Seq (6 bp barcode, no UMI): strt-seq</li>
<li>STRT-Seq-C1 (8 bp barode, 5 bp UMI): strt-seq-c1</li>
<li>STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i</li>
<li>STRT-Seq-2018 (8 bp barcode, 8 bp UMI): strt-seq-2018</li>
</ul></li>
<li>SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad</li>
</ul>
</ul></li>
<li>VASA-Seq
<ul>
<li>VASA-plate (6 bp UMI, 6 bp barcode): vasa-plate</li>
<li>VASA-drop (6 bp UMI, 16 bp barcode): vasa-drop</li>
</ul></li>
<h4 id="chemistry-settings-available">Chemistry settings available</h4>
<p>All technologies support 3′ single-cell RNA-Seq. Barcode adjustments
and whitelists are changed automatically. For 5′ single-cell RNA-Seq,
Expand Down Expand Up @@ -1006,6 +1019,10 @@ <h4 id="help-menu">Help menu</h4>
MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1
MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
PIP-Seq version 1 (16 bp barcode, 6 bp UMI): pip-seq-v1
PIP-Seq version 2 (24 bp barcode, 12 bp UMI): pip-seq-v2
PIP-Seq version 3 (28 bp barcode, 12 bp UMI): pip-seq-v3
PIP-Seq version 4 (28 bp barcode, 12 bp UMI): pip-seq-v4
QuartzSeq (6 bp index, no UMI): quartz-seq
Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536
Expand All @@ -1025,6 +1042,8 @@ <h4 id="help-menu">Help menu</h4>
STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i
STRT-Seq-2018 (8 bp barcode, 8 bp UMI): strt-seq-2018
SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad
VASA-plate (6 bp UMI, 6 bp barcode): vasa-plate
VASA-drop (6 bp UMI, 16 bp barcode): vasa-drop
Custom inputs are also supported by giving the name &quot;custom&quot; and length of barcode and UMI separated by &quot;_&quot;
e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10

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14 changes: 14 additions & 0 deletions README.md
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Expand Up @@ -212,6 +212,11 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
- MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
- Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
- Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq
- PIP-Seq
- PIP-Seq version 1 (16 bp barcode, 6 bp UMI): pip-seq-v1
- PIP-Seq version 2 (24 bp barcode, 12 bp UMI): pip-seq-v2
- PIP-Seq version 3 (28 bp barcode, 12 bp UMI): pip-seq-v3
- PIP-Seq version 4 (28 bp barcode, 12 bp UMI): pip-seq-v4
- Quartz-Seq
- QuartzSeq (6 bp index, no UMI): quartz-seq
- Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
Expand All @@ -236,6 +241,9 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
- STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i
- STRT-Seq-2018 (8 bp barcode, 8 bp UMI): strt-seq-2018
- SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad
- VASA-Seq
- VASA-plate (6 bp UMI, 6 bp barcode): vasa-plate
- VASA-drop (6 bp UMI, 16 bp barcode): vasa-drop

#### Chemistry settings available

Expand Down Expand Up @@ -1192,6 +1200,10 @@ Mandatory arguments to long options are mandatory for short options too.
MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1
MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
PIP-Seq version 1 (16 bp barcode, 6 bp UMI): pip-seq-v1
PIP-Seq version 2 (24 bp barcode, 12 bp UMI): pip-seq-v2
PIP-Seq version 3 (28 bp barcode, 12 bp UMI): pip-seq-v3, fluent-bio-v3
PIP-Seq version 4 (28 bp barcode, 12 bp UMI): pip-seq-v4, fluent-bio-v4
QuartzSeq (6 bp index, no UMI): quartz-seq
Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536
Expand All @@ -1211,6 +1223,8 @@ Mandatory arguments to long options are mandatory for short options too.
STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i
STRT-Seq-2018 (8 bp barcode, 8 bp UMI): strt-seq-2018
SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad
VASA-plate (6 bp UMI, 6 bp barcode): vasa-plate
VASA-drop (6 bp UMI, 16 bp barcode): vasa-drop
Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10
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14 changes: 14 additions & 0 deletions README.txt
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Expand Up @@ -212,6 +212,11 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
- MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
- Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
- Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq
- PIP-Seq
- PIP-Seq version 1 (16 bp barcode, 6 bp UMI): pip-seq-v1
- PIP-Seq version 2 (24 bp barcode, 12 bp UMI): pip-seq-v2
- PIP-Seq version 3 (28 bp barcode, 12 bp UMI): pip-seq-v3
- PIP-Seq version 4 (28 bp barcode, 12 bp UMI): pip-seq-v4
- Quartz-Seq
- QuartzSeq (6 bp index, no UMI): quartz-seq
- Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
Expand All @@ -236,6 +241,9 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
- STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i
- STRT-Seq-2018 (8 bp barcode, 8 bp UMI): strt-seq-2018
- SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad
- VASA-Seq
- VASA-plate (6 bp UMI, 6 bp barcode): vasa-plate
- VASA-drop (6 bp UMI, 16 bp barcode): vasa-drop

#### Chemistry settings available

Expand Down Expand Up @@ -1192,6 +1200,10 @@ Mandatory arguments to long options are mandatory for short options too.
MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1
MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
PIP-Seq version 1 (16 bp barcode, 6 bp UMI): pip-seq-v1
PIP-Seq version 2 (24 bp barcode, 12 bp UMI): pip-seq-v2
PIP-Seq version 3 (28 bp barcode, 12 bp UMI): pip-seq-v3, fluent-bio-v3
PIP-Seq version 4 (28 bp barcode, 12 bp UMI): pip-seq-v4, fluent-bio-v4
QuartzSeq (6 bp index, no UMI): quartz-seq
Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384
Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536
Expand All @@ -1211,6 +1223,8 @@ Mandatory arguments to long options are mandatory for short options too.
STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i
STRT-Seq-2018 (8 bp barcode, 8 bp UMI): strt-seq-2018
SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad
VASA-plate (6 bp UMI, 6 bp barcode): vasa-plate
VASA-drop (6 bp UMI, 16 bp barcode): vasa-drop
Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10

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14 changes: 10 additions & 4 deletions man/launch_universc.sh
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Expand Up @@ -234,6 +234,10 @@ Provides a conversion script to run multiple technologies and custom libraries w
MARS-Seq (6 bp barcode, 10 bp UMI): marsseq, marsseq-v1
MARS-Seq2 (7 bp barcode, 8 bp UMI): marsseq2, marsseq-v2
Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
PIP-Seq version 1 (16 bp barcode, 6 bp UMI): pip-seq-v1
PIP-Seq version 2 (24 bp barcode, 12 bp UMI): pip-seq-v2
PIP-Seq version 3 (28 bp barcode, 12 bp UMI): pip-seq-v3, fluent-bio-v3
PIP-Seq version 4 (28 bp barcode, 12 bp UMI): pip-seq-v4, fluent-bio-v4
QuartzSeq (6 bp index, no UMI): quartz-seq
Quartz-Seq2 (14 bp barcode, 8bp UMI): quartzseq2-384
Quartz-Seq2 (15 bp barcode, 8bp UMI): quartzseq2-1536
Expand All @@ -248,11 +252,13 @@ Provides a conversion script to run multiple technologies and custom libraries w
Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3
SPLiT-Seq (8 bp UMI, 24 bp barcode): splitseq
SPLiT-Seq v2.1 (10 bp UMI, 24 bp barcode): splitseq2
STRT-Seq (6 bp barcode, no UMI)
STRT-Seq-C1 (8 bp barode, 5 bp UMI)
STRT-Seq-2i (13 bp barcode, 6 bp UMI)
STRT-Seq-2018 (8 bp barcode, 8 bp UMI)
STRT-Seq (6 bp barcode, no UMI): strt-seq
STRT-Seq-C1 (8 bp barode, 5 bp UMI): strt-seq-c1
STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i
STRT-Seq-2018 (8 bp barcode, 8 bp UMI): strt-seq-2019
SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad
VASA-plate (6 bp UMI, 6 bp barcode): vasa-plate
VASA-drop (6 bp UMI, 16 bp barcode): vasa-drop
Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10
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