make experimental technologies (not fully supported) clear in docs (b71930e3) · Commits · github_fork / Universc

README.Rmd

+6 −3

Original line number	Diff line number	Diff line
		@@ -952,18 +952,21 @@ Mandatory arguments to long options are mandatory for short options too.
		ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom
		inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1
		inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2
		inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1
		MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq
		SeqWell (12bp barcode, 8bp UMI): seqwell
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq
		SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10

		Experimental technologies (not yet supported):
		inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq

		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)

		-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: SC3Pv2 (default), SC5P-PE, or SC5P-R2

README.html

+12 −11

Original line number	Diff line number	Diff line
		@@ -338,18 +338,16 @@ git lfs install</code></pre>
		<p>To import large files from Github change to the "universc" directory and run:</p>
		<pre><code>git lfs pull origin</code></pre>
		<p>This provides almost all files required. The STAR index and reference need to be generated or imported from an existing reference. The following code detects whether the references are available in an existing cellranger installation.</p>
		<pre><code>cd test
		cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2 -d'(' \| cut -f1 -d')'`
		<pre><code>cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2 -d'(' \| cut -f1 -d')'`
		cellrangerpath=`which cellranger`

		# set up cellranger reference
		if [[ ! -f ${cellrangerpath}-${cellrangerversion}/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 ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA
		fi
		if [[ ! -f ${cellrangerpath}-${cellrangerversion}/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 ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA
		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
		cd ..</code></pre>
		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
		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>
		@@ -469,18 +467,21 @@ Mandatory arguments to long options are mandatory for short options too.
		ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom
		inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1
		inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2
		inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1
		MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq
		SeqWell (12bp barcode, 8bp UMI): seqwell
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq
		SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10

		Experimental technologies (not yet supported):
		inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq

		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)

		-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: SC3Pv2 (default), SC5P-PE, or SC5P-R2

README.md

+12 −11

Original line number	Diff line number	Diff line
		@@ -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: "Wednesday 20 January 2021"
		date: "Friday 22 January 2021"
		output:
		prettydoc::html_pretty:
		theme: cayman
		@@ -32,7 +32,7 @@ tags:
		![Docker Automated build](https://img.shields.io/docker/automated/tomkellygenetics/universc)
		![Docker Build Status](https://img.shields.io/docker/build/tomkellygenetics/universc)
		![Docker Image Size (tag)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/latest)
		[![GitHub Views](http://hits.dwyl.com/minoda-lab/universc.svg)](http://hits.dwyl.com/minoda-lab/universc)
		[![GitHub Views](http://hits.dwyl.com/tomkellygenetics/universc.svg)](http://hits.dwyl.com/tomkellygenetics/universc)

		![Docker Stars](https://img.shields.io/docker/stars/tomkellygenetics/universc)
		![Docker Pulls](https://img.shields.io/docker/pulls/tomkellygenetics/universc)
		@@ -754,18 +754,16 @@ imported from an existing reference. The following code detects whether the refe
		available in an existing cellranger installation.

		```
		cd test
		cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2 -d'(' \| cut -f1 -d')'`
		cellrangerpath=`which cellranger`

		# set up cellranger reference
		if [[ ! -f ${cellrangerpath}-${cellrangerversion}/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 ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/3.0.0/star/SA
		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 ${cellrangerpath}-${cellrangerversion}/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 ${cellrangerpath}-${cellrangerversion}/cellranger-tiny-ref/1.2.0/star/SA
		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
		fi
		cd ..
		```

		This creates a reference for Cell Ranger here:
		@@ -954,18 +952,21 @@ Mandatory arguments to long options are mandatory for short options too.
		ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom
		inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1
		inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2
		inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1
		MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq
		SeqWell (12bp barcode, 8bp UMI): seqwell
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq
		SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10

		Experimental technologies (not yet supported):
		inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq

		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)

		-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: SC3Pv2 (default), SC5P-PE, or SC5P-R2

launch_universc.sh

+6 −3

Original line number	Diff line number	Diff line
		@@ -203,19 +203,22 @@ Mandatory arguments to long options are mandatory for short options too.
		ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom
		inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1
		inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2
		inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1
		MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq
		SeqWell (12bp barcode, 8bp UMI): seqwell
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq
		SPLiT-Seq (10bp UMI, 18bp barcode): splitseq
		SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10

		Experimental technologies (not yet supported):
		inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq

		-b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode)

		-c, --chemistry CHEM Assay configuration, autodetection is not possible for converted files: 'SC3Pv2' (default), 'SC5P-PE', or 'SC5P-R2'

man/launch_universc.sh

+5 −3

Original line number	Diff line number	Diff line
		@@ -193,20 +193,22 @@ Provides a conversion script to run multiple technologies and custom libraries w
		ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom
		inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1
		inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2
		inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1
		MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2
		Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384
		Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq
		SeqWell (12bp barcode, 8bp UMI): seqwell
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq
		SPLiT-Seq (10bp UMI, 18bp barcode): splitseq
		SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
		Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"
		e.g. Custom (16bp barcode, 10bp UMI): custom_16_10

		Experimental technologies (not yet supported):
		inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3
		Sci-Seq (8bp UMI, 10bp barcode): sciseq
		Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq

		A barcode whitelist is provided for all beads or wells for the following technologies:

		10x Genomics, ICELL8, inDrops-v2, and QuartzSeq2

Admin message