Commit ba6cb1b8 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

clarify technologies in documentation

parent cc17f0d5

README.Rmd

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@@ -134,6 +134,23 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  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

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.



#### Dual-indexing



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

before calling UniverSC:



```

   /usr/local/bin/bcl2fastq  -v --runfolder-dir "/path/to/illumina/bcls"  --output-dir "./Data/Intensities/BaseCalls"\

                                --sample-sheet "/path/to/SampleSheet.csv" --create-fastq-for-index-reads\

                                --use-bases-mask Y26n,I8n,I8n,Y50n  --mask-short-adapter-reads 0\

                                --minimum-trimmed-read-length 0

```



#### Custom inputs



Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by a "_" character.

README.html

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<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>

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

<p>For dual-indexed technologies such as inDrops-v3, Sci-Seq, SmartSeq3 it is advised to use “bcl2fastq” 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;\

                                --sample-sheet &quot;/path/to/SampleSheet.csv&quot; --create-fastq-for-index-reads\

                                --use-bases-mask Y26n,I8n,I8n,Y50n  --mask-short-adapter-reads 0\

                                --minimum-trimmed-read-length 0</code></pre>

<h4 id="custom-inputs">Custom inputs</h4>

<p>Custom inputs are also supported by giving the name “custom” and length of barcode and UMI separated by a &quot;_&quot; character.</p>

<p>e.g. Custom (16bp barcode, 10bp UMI): <code>custom_16_10</code></p>

README.md

+17 −0
Original line number Diff line number Diff line
@@ -134,6 +134,23 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  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

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.



#### Dual-indexing



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

before calling UniverSC:



```

   /usr/local/bin/bcl2fastq  -v --runfolder-dir "/path/to/illumina/bcls"  --output-dir "./Data/Intensities/BaseCalls"\

                                --sample-sheet "/path/to/SampleSheet.csv" --create-fastq-for-index-reads\

                                --use-bases-mask Y26n,I8n,I8n,Y50n  --mask-short-adapter-reads 0\

                                --minimum-trimmed-read-length 0

```



#### Custom inputs



Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by a "_" character.

man/convert.sh

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@@ -132,14 +132,13 @@ Provides a conversion script to run multiple technologies and custom libraries w 


            Or



                /usr/local/bin/bcl2fastq -v --runfolder-dir "/path/to/illumina/bcls"  --output-dir "./Data/Intensities/BaseCalls"\

                                            --sample-sheet "/path/to/SampleSheet.csv" --create-fastq-for-index-reads



                /usr/local/bin/bcl2fastq  -v --runfolder-dir "/path/to/illumina/bcls"  --output-dir "./Data/Intensities/BaseCalls"\

                                             --sample-sheet "/path/to/SampleSheet.csv" --create-fastq-for-index-reads\

                                             --use-bases-mask Y26n,I8n,I8n,Y50n  --mask-short-adapter-reads 0\

                                             --minimum-trimmed-read-length 0



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



            Note that dual indexes are not supported by cellranger. Manually demultiplexing as above into separate

            FASTQ files before processing should work as multiple samples are supported. For example, files names as:

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