Commit cbbd55bc authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

document inputs for non-UMI technologies

parent e2d0d0d5

README.Rmd

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@@ -205,10 +205,10 @@ 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):

-  ICELL8 (11 bp barcode, no UMI)

-  RamDA-Seq (6 bp index, no UMI)

-  QuartzSeq (6 bp index, no UMI)

-  SmartSeq2 (16 bp barcode, no UMI)

-  ICELL8 (11 bp barcode, no UMI): icell8-non-umi, icell8-v2

-  RamDA-Seq (6 bp index, no UMI): ramda-seq

-  QuartzSeq (6 bp index, no UMI): quartz-seq

-  SmartSeq2 (16 bp barcode, no UMI): smartseq, smartseq2





#### Dual-indexing
@@ -1038,10 +1038,10 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10



                                Experimental

                                  ICELL8 (11 bp barcode, no UMI)

                                  RamDA-Seq (6 bp index, no UMI)

                                  QuartzSeq (6 bp index, no UMI)

                                  SmartSeq2 (16 bp barcode, no UMI)

                                  ICELL8 (11 bp barcode, no UMI): icell8-non-umi, icell8-v2

                                  RamDA-Seq (6 bp index, no UMI): ramda-seq

                                  QuartzSeq (6 bp index, no UMI): quartz-seq

                                  SmartSeq2 (16 bp barcode, no UMI): smartseq2



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

README.html

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@@ -92,7 +92,7 @@ 
</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): - ICELL8 (11 bp barcode, no UMI) - RamDA-Seq (6 bp index, no UMI) - QuartzSeq (6 bp index, no UMI) - SmartSeq2 (16 bp barcode, no UMI)</p>

<p>Experimental technologies (not yet supported): - ICELL8 (11 bp barcode, no UMI): icell8-non-umi, icell8-v2 - RamDA-Seq (6 bp index, no UMI): ramda-seq - QuartzSeq (6 bp index, no UMI): quartz-seq - SmartSeq2 (16 bp barcode, no UMI): smartseq, smartseq2</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;\
@@ -521,10 +521,10 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10



                                Experimental

                                  ICELL8 (11 bp barcode, no UMI)

                                  RamDA-Seq (6 bp index, no UMI)

                                  QuartzSeq (6 bp index, no UMI)

                                  SmartSeq2 (16 bp barcode, no UMI)

                                  ICELL8 (11 bp barcode, no UMI): icell8-non-umi, icell8-v2

                                  RamDA-Seq (6 bp index, no UMI): ramda-seq

                                  QuartzSeq (6 bp index, no UMI): quartz-seq

                                  SmartSeq2 (16 bp barcode, no UMI): smartseq2



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

README.md

+8 −8
Original line number Diff line number Diff line
@@ -205,10 +205,10 @@ 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):

-  ICELL8 (11 bp barcode, no UMI)

-  RamDA-Seq (6 bp index, no UMI)

-  QuartzSeq (6 bp index, no UMI)

-  SmartSeq2 (16 bp barcode, no UMI)

-  ICELL8 (11 bp barcode, no UMI): icell8-non-umi, icell8-v2

-  RamDA-Seq (6 bp index, no UMI): ramda-seq

-  QuartzSeq (6 bp index, no UMI): quartz-seq

-  SmartSeq2 (16 bp barcode, no UMI): smartseq, smartseq2





#### Dual-indexing
@@ -1038,10 +1038,10 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10



                                Experimental

                                  ICELL8 (11 bp barcode, no UMI)

                                  RamDA-Seq (6 bp index, no UMI)

                                  QuartzSeq (6 bp index, no UMI)

                                  SmartSeq2 (16 bp barcode, no UMI)

                                  ICELL8 (11 bp barcode, no UMI): icell8-non-umi, icell8-v2

                                  RamDA-Seq (6 bp index, no UMI): ramda-seq

                                  QuartzSeq (6 bp index, no UMI): quartz-seq

                                  SmartSeq2 (16 bp barcode, no UMI): smartseq2



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

launch_universc.sh

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@@ -226,10 +226,10 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10



                                Experimental

                                  ICELL8 (11 bp barcode, no UMI)

                                  RamDA-Seq (6 bp index, no UMI)

                                  QuartzSeq (6 bp index, no UMI)

                                  SmartSeq2 (16 bp barcode, no UMI)

                                  ICELL8 (11 bp barcode, no UMI): icell8-non-umi, icell8-v2

                                  RamDA-Seq (6 bp index, no UMI): ramda-seq

                                  QuartzSeq (6 bp index, no UMI): quartz-seq

                                  SmartSeq2 (16 bp barcode, no UMI): smartseq, smartseq2



  -b,  --barcodefile FILE       Custom barcode list in plain text (with each line containing a barcode)
@@ -620,9 +620,9 @@ elif [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "bd" ]] || [[ " 
    technology="bd-rhapsody"

elif [[ "$technology" == "nadia" ]] || [[ "$technology" == "dropseq" ]] || [[ "$technology" == "drop-seq" ]]; then

    technology="nadia"

elif [[ "$technology" == "icell8" ]] || [[ "$technology" == "icell-8" ]]; then

elif [[ "$technology" == "icell8" ]] || [[ "$technology" == "icell-8" ]] ||  [[ "$technology" == "icell8-v3" ]] ||  [[ "$technology" == "icell8v3" ]]; then

    technology="icell8"

elif [[ "$technology" == "icell8-non-umi" ]] || [[ "$technology" == "icell8-nonumi" ]]; then

elif [[ "$technology" == "icell8-non-umi" ]] || [[ "$technology" == "icell8-nonumi" ]] ||  [[ "$technology" == "icell8-v2" ]] ||  [[ "$technology" == "icell8v2" ]]; then

    technology="icell8"

    nonUMI=true

elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrops-v1" ]] || [[ "$technology" == "indropv1" ]] || [[ "$technology" == "indropsv1" ]] || [[ "$technology" == "1cellbio-v1" ]] || [[ "$technology" == "1cellbiov1" ]]; then

man/launch_universc.sh

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@@ -216,10 +216,10 @@ Provides a conversion script to run multiple technologies and custom libraries w 
                                  e.g. Custom (16 bp barcode, 10 bp UMI): custom_16_10



                                Experimental

                                  ICELL8 (11 bp barcode, no UMI)

                                  RamDA-Seq (6 bp index, no UMI)

                                  QuartzSeq (6 bp index, no UMI)

                                  SmartSeq2 (16 bp barcode, no UMI)

                                  ICELL8 (11 bp barcode, no UMI): icell8-non-umi, icell8-v2

                                  RamDA-Seq (6 bp index, no UMI) ramda-seq

                                  QuartzSeq (6 bp index, no UMI): quartz-seq

                                  SmartSeq2 (16 bp barcode, no UMI):smart-seq2



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

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