Commit a2109417 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update documentation to include dual-indexed and combinatorial indexing technologies

parent 10f89e4d

README.Rmd

+40 −28
Original line number Diff line number Diff line
@@ -164,6 +164,8 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  10x Genomics (version automatically detected): 10x, chromium

    -  10x Genomics version 2 (16bp barcode, 10bp UMI): 10x-v2, chromium-v2

    -  10x Genomics version 3 (16bp barcode, 12bp UMI): 10x-v3, chromium-v3

-  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

-  CEL-Seq

    -  CEL-Seq  (8bp barcode, 4bp UMI): celseq

    -  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

-  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq
@@ -171,14 +173,29 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  inDrops

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

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

    -  inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3

 -  MARS-Seq

    -  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

-  Quartz-Seq

    -  Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384

    -  Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536

-  Single-cell combinatorial indexing

   -  SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2

   -  SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3

   -  SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq

-  SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq

-  SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3

-  Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2

-  SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq

-  Smart-seq

   -  Smart-seq2 (16 bp barcode, No UMI): smartseq2

   -  Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3

-  STRT-Seq

    -  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)

-  SureCell (18 bp barcode, 8 bp 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
@@ -188,18 +205,12 @@ 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):

-  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

-  inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

-  Microwell-Seq (18 bp barcode, 6 bp UMI): microwell

-  SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2

-  SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3

-  SPLiT-Seq (10bp UMI, 24 bp barcode): splitseq

-  SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad

-  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)

-  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)





#### Dual-indexing



For dual-indexed technologies such as inDrops-v3, Sci-Seq, SmartSeq3 it is advised to use "bcl2fastq"
@@ -998,6 +1009,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  10x Genomics (version automatically detected): 10x, chromium

                                  10x Genomics version 2 (16bp barcode, 10bp UMI): 10x-v2, chromium-v2

                                  10x Genomics version 3 (16bp barcode, 12bp UMI): 10x-v3, chromium-v3

                                  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

                                  CEL-Seq (8bp barcode, 4bp UMI): celseq

                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

                                  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq
@@ -1007,27 +1019,27 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  inDrops version 3 (16bp 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   

                                  Microwell-Seq (18 bp barcode, 6 bp UMI): microwell

                                  Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384

                                  Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536

                                  SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2

                                  SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3

                                  SCIFI-Seq (27 bp barcode, 8 bp UMI

                                  SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq

                                  SeqWell (12bp barcode, 8bp UMI): plexwell, seqwell, seqwells3

                                  Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2

                                  Smart-seq2-UMI, Smart-seq3 (16bp barcode, 8bp UMI): smartseq3

                                  SPLiT-Seq (10bp UMI, 24bp barcode): splitseq

                                  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)

                                  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

                                  Microwell-Seq (18 bp barcode, 6 bp UMI): microwell

                                  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

                                  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)

                                  ICELL8 (11 bp barcode, no UMI)

                                  SmartSeq2 (16 bp barcode, no UMI)

                                  SCIFI-Seq (27 bp barcode, 8 bp UMI



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

README.html

+43 −17
Original line number Diff line number Diff line
@@ -46,28 +46,53 @@ 
<li>10x Genomics version 2 (16bp barcode, 10bp UMI): 10x-v2, chromium-v2</li>

<li>10x Genomics version 3 (16bp barcode, 12bp UMI): 10x-v3, chromium-v3</li>

</ul></li>

<li>BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody</li>

<li>CEL-Seq

<ul>

<li>CEL-Seq (8bp barcode, 4bp UMI): celseq</li>

<li>CEL-Seq2 (6bp UMI, 6bp barcode): celseq2</li>

</ul></li>

<li>Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq</li>

<li>ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom</li>

<li>inDrops

<ul>

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

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

<li>inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3</li>

</ul></li>

<li>MARS-Seq

<ul>

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

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

</li>

</ul></li>

<li>Microwell-Seq (18 bp barcode, 6 bp UMI): microwell</li>

<li>Quartz-Seq

<ul>

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

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

</ul></li>

<li>Single-cell combinatorial indexing</li>

<li>SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2</li>

<li>SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3</li>

<li>SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq</li>

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

<li>SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3</li>

<li>Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2</li>

<li>SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq</li>

<li>Smart-seq</li>

<li>Smart-seq2 (16 bp barcode, No UMI): smartseq2</li>

<li>Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3</li>

<li>STRT-Seq

<ul>

<li>STRT-Seq (6 bp barcode, no UMI)</li>

<li>STRT-Seq-C1 (8 bp barode, 5 bp UMI)</li>

<li>STRT-Seq-2i (13 bp barcode, 6 bp UMI)</li>

</ul></li>

<li>SureCell (18 bp barcode, 8 bp 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): - BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody - inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 - Microwell-Seq (18 bp barcode, 6 bp UMI): microwell - SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2 - SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3 - SPLiT-Seq (10bp UMI, 24 bp barcode): splitseq - SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad - 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) - SmartSeq2 (16 bp barcode, no UMI)</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>

<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;\
@@ -467,6 +492,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  10x Genomics (version automatically detected): 10x, chromium

                                  10x Genomics version 2 (16bp barcode, 10bp UMI): 10x-v2, chromium-v2

                                  10x Genomics version 3 (16bp barcode, 12bp UMI): 10x-v3, chromium-v3

                                  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

                                  CEL-Seq (8bp barcode, 4bp UMI): celseq

                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

                                  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq
@@ -476,27 +502,27 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  inDrops version 3 (16bp 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   

                                  Microwell-Seq (18 bp barcode, 6 bp UMI): microwell

                                  Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384

                                  Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536

                                  SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2

                                  SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3

                                  SCIFI-Seq (27 bp barcode, 8 bp UMI

                                  SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq

                                  SeqWell (12bp barcode, 8bp UMI): plexwell, seqwell, seqwells3

                                  Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2

                                  Smart-seq2-UMI, Smart-seq3 (16bp barcode, 8bp UMI): smartseq3

                                  SPLiT-Seq (10bp UMI, 24bp barcode): splitseq

                                  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)

                                  SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad

                                Custom inputs are also supported by giving the name &quot;custom&quot; and length of barcode and UMI separated by &quot;_&quot;

                                  e.g. Custom (16bp barcode, 10bp UMI): custom_16_10



                                Experimental

                                  Microwell-Seq (18 bp barcode, 6 bp UMI): microwell

                                  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

                                  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)

                                  ICELL8 (11 bp barcode, no UMI)

                                  SmartSeq2 (16 bp barcode, no UMI)

                                  SCIFI-Seq (27 bp barcode, 8 bp UMI



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

README.md

+40 −28
Original line number Diff line number Diff line
@@ -164,6 +164,8 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  10x Genomics (version automatically detected): 10x, chromium

    -  10x Genomics version 2 (16bp barcode, 10bp UMI): 10x-v2, chromium-v2

    -  10x Genomics version 3 (16bp barcode, 12bp UMI): 10x-v3, chromium-v3

-  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

-  CEL-Seq

    -  CEL-Seq  (8bp barcode, 4bp UMI): celseq

    -  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

-  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq
@@ -171,14 +173,29 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  inDrops

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

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

    -  inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3

 -  MARS-Seq

    -  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

-  Quartz-Seq

    -  Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384

    -  Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536

-  Single-cell combinatorial indexing

   -  SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2

   -  SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3

   -  SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq

-  SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq

-  SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3

-  Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2

-  SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq

-  Smart-seq

   -  Smart-seq2 (16 bp barcode, No UMI): smartseq2

   -  Smart-seq2-UMI, Smart-seq3 (16 bp barcode, 8 bp UMI): smartseq3

-  STRT-Seq

    -  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)

-  SureCell (18 bp barcode, 8 bp 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
@@ -188,18 +205,12 @@ 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):

-  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

-  inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

-  Microwell-Seq (18 bp barcode, 6 bp UMI): microwell

-  SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2

-  SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3

-  SPLiT-Seq (10bp UMI, 24 bp barcode): splitseq

-  SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad

-  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)

-  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)





#### Dual-indexing



For dual-indexed technologies such as inDrops-v3, Sci-Seq, SmartSeq3 it is advised to use "bcl2fastq"
@@ -998,6 +1009,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  10x Genomics (version automatically detected): 10x, chromium

                                  10x Genomics version 2 (16bp barcode, 10bp UMI): 10x-v2, chromium-v2

                                  10x Genomics version 3 (16bp barcode, 12bp UMI): 10x-v3, chromium-v3

                                  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

                                  CEL-Seq (8bp barcode, 4bp UMI): celseq

                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

                                  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq
@@ -1007,27 +1019,27 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  inDrops version 3 (16bp 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   

                                  Microwell-Seq (18 bp barcode, 6 bp UMI): microwell

                                  Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384

                                  Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536

                                  SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2

                                  SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3

                                  SCIFI-Seq (27 bp barcode, 8 bp UMI

                                  SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq

                                  SeqWell (12bp barcode, 8bp UMI): plexwell, seqwell, seqwells3

                                  Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2

                                  Smart-seq2-UMI, Smart-seq3 (16bp barcode, 8bp UMI): smartseq3

                                  SPLiT-Seq (10bp UMI, 24bp barcode): splitseq

                                  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)

                                  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

                                  Microwell-Seq (18 bp barcode, 6 bp UMI): microwell

                                  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

                                  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)

                                  ICELL8 (11 bp barcode, no UMI)

                                  SmartSeq2 (16 bp barcode, no UMI)

                                  SCIFI-Seq (27 bp barcode, 8 bp UMI



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

launch_universc.sh

+11 −8
Original line number Diff line number Diff line
@@ -197,6 +197,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  10x Genomics (version automatically detected): 10x, chromium

                                  10x Genomics version 2 (16bp barcode, 10bp UMI): 10x-v2, chromium-v2

                                  10x Genomics version 3 (16bp barcode, 12bp UMI): 10x-v3, chromium-v3

                                  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

                                  CEL-Seq (8bp barcode, 4bp UMI): celseq

                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

                                  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq
@@ -206,27 +207,29 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  inDrops version 3 (16bp 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   

                                  Microwell-Seq (18 bp barcode, 6 bp UMI): microwell

                                  Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384

                                  Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536

                                  SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2

                                  SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3

                                  SCIFI-Seq (27 bp barcode, 8 bp UMI

                                  SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq

                                  SeqWell (12bp barcode, 8bp UMI): plexwell, seqwell, seqwells3

                                  Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2

                                  Smart-seq2-UMI, Smart-seq3 (16bp barcode, 8bp UMI): smartseq3

                                  SPLiT-Seq (10bp UMI, 24bp barcode): splitseq

                                  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)

                                  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

                                   Microwell-Seq (18 bp barcode, 6 bp UMI): microwell

                                   BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

                                   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)

                                  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)

                                   SCIFI-Seq (27 bp barcode, 8 bp UMI



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

man/launch_universc.sh

+10 −7
Original line number Diff line number Diff line
@@ -187,6 +187,7 @@ Provides a conversion script to run multiple technologies and custom libraries w 
                                  10x Genomics (version automatically detected): 10x, chromium

                                  10x Genomics version 2 (16bp barcode, 10bp UMI): 10x-v2, chromium-v2

                                  10x Genomics version 3 (16bp barcode, 12bp UMI): 10x-v3, chromium-v3

                                  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

                                  CEL-Seq (8bp barcode, 4bp UMI): celseq

                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

                                  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq
@@ -196,27 +197,29 @@ Provides a conversion script to run multiple technologies and custom libraries w 
                                  inDrops version 3 (16bp 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   

                                  Microwell-Seq (18 bp barcode, 6 bp UMI): microwell

                                  Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384

                                  Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536

                                  SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2

                                  SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3

                                  SCIFI-Seq (27 bp barcode, 8 bp UMI

                                  SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq

                                  SeqWell (12bp barcode, 8bp UMI): plexwell, seqwell, seqwells3

                                  Smart-seq, Smart-seq2 (16bp barcode, No UMI): smartseq2

                                  Smart-seq2-UMI, Smart-seq3 (16bp barcode, 8bp UMI): smartseq3

                                  SPLiT-Seq (10bp UMI, 24bp barcode): splitseq

                                  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)

                                  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

                                   Microwell-Seq (18 bp barcode, 6 bp UMI): microwell

                                   BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

                                   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)

                                  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)

                                   SCIFI-Seq (27 bp barcode, 8 bp UMI



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

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