Commit 1d7db3b8 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

make experimental technologies (not fully supported) clear in docs

parent b71930e3

README.Rmd

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@@ -132,15 +132,12 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  inDrops

    -  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



All technologies support 3' single-cell RNA-Seq. Barcode adjustments and
@@ -148,6 +145,13 @@ whitelists are changed automatically. For 5' single-cell RNA-Seq, this 
is only supported for 10x Genomics version 2 chemistry. This is detected

automatically but can be configured with the `--chemistry` argument.



We are developing technologies to support dual indexes and full length scRNA kits.



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



#### Dual-indexing



For dual-indexed technologies such as inDrops-v3, Sci-Seq, SmartSeq3 it is advised to use "bcl2fastq"

README.html

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@@ -48,20 +48,19 @@ 
<ul>

<li>inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1</li>

<li>inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2</li>

<li>inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3</li>

</ul></li>

<li>MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1</li>

<li>MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2<br />

</li>

<li>Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384</li>

<li>Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536</li>

<li>Sci-Seq (8bp UMI, 10bp barcode): sciseq</li>

<li>SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq</li>

<li>SeqWell (12bp barcode, 8bp UMI): seqwell</li>

<li>Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq</li>

<li>SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad</li>

</ul>

<p>All technologies support 3' single-cell RNA-Seq. Barcode adjustments and whitelists are changed automatically. For 5' single-cell RNA-Seq, this is only supported for 10x Genomics version 2 chemistry. This is detected automatically but can be configured with the <code>--chemistry</code> argument.</p>

<p>We are developing technologies to support dual indexes and full length scRNA kits.</p>

<p>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</p>

<h4 id="dual-indexing">Dual-indexing</h4>

<p>For dual-indexed technologies such as inDrops-v3, Sci-Seq, SmartSeq3 it is advised to use &quot;bcl2fastq&quot; before calling UniverSC:</p>

<pre><code>   /usr/local/bin/bcl2fastq  -v --runfolder-dir &quot;/path/to/illumina/bcls&quot;  --output-dir &quot;./Data/Intensities/BaseCalls&quot;\

README.md

+7 −3
Original line number Diff line number Diff line
@@ -132,15 +132,12 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  inDrops

    -  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



All technologies support 3' single-cell RNA-Seq. Barcode adjustments and
@@ -148,6 +145,13 @@ whitelists are changed automatically. For 5' single-cell RNA-Seq, this 
is only supported for 10x Genomics version 2 chemistry. This is detected

automatically but can be configured with the `--chemistry` argument.



We are developing technologies to support dual indexes and full length scRNA kits.



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



#### Dual-indexing



For dual-indexed technologies such as inDrops-v3, Sci-Seq, SmartSeq3 it is advised to use "bcl2fastq"

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