From acbf266ae12ccd2a3f48bb8b6cee922d88ed3f57 Mon Sep 17 00:00:00 2001 From: TomKellyGenetics Date: Tue, 19 Sep 2023 00:47:36 +0900 Subject: [PATCH] add PIP-Seq and VASA-Seq to documentation (work-in-progress) --- CHANGELOG | 2 ++ README.Rmd | 14 ++++++++++++++ README.html | 21 ++++++++++++++++++++- README.md | 14 ++++++++++++++ README.txt | 14 ++++++++++++++ man/launch_universc.sh | 14 ++++++++++---- 6 files changed, 74 insertions(+), 5 deletions(-) diff --git a/CHANGELOG b/CHANGELOG index 03c04f5..17a518f 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -3,6 +3,8 @@ - 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 diff --git a/README.Rmd b/README.Rmd index 057c3f9..62fd78d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -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 @@ -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 @@ -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 @@ -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 diff --git a/README.html b/README.html index bb935c2..7081d7a 100644 --- a/README.html +++ b/README.html @@ -277,6 +277,13 @@

Pre-set configurations

  • Microwell-Seq (18 bp barcode, 6 bp UMI): microwell
  • Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq
    • +
  • PIP-Seq +
  • Quartz-Seq
  • SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad
    • - + +
  • VASA-Seq +

    • Chemistry settings available

    All technologies support 3′ single-cell RNA-Seq. Barcode adjustments and whitelists are changed automatically. For 5′ single-cell RNA-Seq, @@ -1006,6 +1019,10 @@

    Help menu

    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 @@ -1025,6 +1042,8 @@

    Help menu

    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 diff --git a/README.md b/README.md index ff63da6..3fee424 100644 --- a/README.md +++ b/README.md @@ -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 @@ -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 @@ -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 @@ -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 diff --git a/README.txt b/README.txt index ff63da6..3fee424 100644 --- a/README.txt +++ b/README.txt @@ -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 @@ -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 @@ -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 @@ -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 diff --git a/man/launch_universc.sh b/man/launch_universc.sh index 0a6956e..aaab128 100755 --- a/man/launch_universc.sh +++ b/man/launch_universc.sh @@ -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 @@ -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