Commit 5a56d17a authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update technologies in documentation

parent 1cc911db

README.Rmd

+33 −18
Original line number Diff line number Diff line
@@ -168,7 +168,9 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  CEL-Seq

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

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

-  Drop-Seq (12 bp barcode, 8 bp UMI): nadia, dropseq

-  Drop-Seq (12 bp barcode, 8 bp UMI): dropseq

-  ICELL8

    -  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

    -  ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom

-  inDrops

    -  inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1
@@ -178,10 +180,13 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
    -  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

-  Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq

-  Quartz-Seq

    -  QuartzSeq (6 bp index, no UMI): 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

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

-  Single-cell combinatorial indexing (SCI-RNA-Seq)

   -  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
@@ -189,8 +194,9 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3

-  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

   -  Smart-Seq (16 bp barcode, No UMI): smartseq

   -  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)
@@ -199,17 +205,17 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 


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.



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



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



is only supported for 10x Genomics version 2 chemistry, ICELL8, 

Smart-Seq, and STRT-Seq.

For 10x Genomics, this is detected automatically but can be

configured with the `--chemistry` argument.

For other technologies, the template switching oligonucleotide

is automatically converted to the match the 10x sequence. 



Single indexes are supported for STRT-Seq, Quartz-Seq, and RamDA-Seq.

Dual indexes are supported for inDrops-v3, SCI-RNA-Seq, scifi-seq, and Smart-Seq.

Combinatorial indexing technologies have linkers between barcodes removed

automatically to match the barcode whitelist.



#### Dual-indexing
@@ -232,6 +238,10 @@ Custom inputs are also supported by giving the name "custom" and length of barco 
Custom barcode files are also supported for preset technologies. These are particularly useful for well-based

technologies to demutliplex based on the wells.



Note that custom inputs do not remove linker or adapter sequences for combinatorial indexng technologies.

These must be removed from the Read 1 file before running UniverSC. To request a preset technology

setting instead, please submit a feature request on GitHub as described below.



## Release



This tool will be released open-source (see [legal stuff](#licensing) below).
@@ -1012,22 +1022,27 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

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

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

                                  Drop-Seq (12 bp barcode, 8 bp UMI): nadia, dropseq

                                  Drop-Seq (12 bp barcode, 8 bp UMI): dropseq

                                  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

                                  ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom

                                  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

                                  Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq

                                  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

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

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

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

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

                                  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 (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq

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

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

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

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

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

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

                                  STRT-Seq (6 bp barcode, no UMI)

README.html

+22 −9
Original line number Diff line number Diff line
@@ -52,8 +52,12 @@ 
<li>CEL-Seq (8 bp barcode, 4 bp UMI): celseq</li>

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

</ul></li>

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

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

<li>ICELL8

<ul>

<li>ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2</li>

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

</ul></li>

<li>inDrops

<ul>

<li>inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1</li>
@@ -67,12 +71,15 @@ 
</li>

</ul></li>

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

<li>Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq</li>

<li>Quartz-Seq

<ul>

<li>QuartzSeq (6 bp index, no UMI): quartz-seq</li>

<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>RamDA-Seq (6 bp index, no UMI): ramda-seq</li>

<li>Single-cell combinatorial indexing (SCI-RNA-Seq)</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>
@@ -80,8 +87,9 @@ 
<li>SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3</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>Smart-Seq (16 bp barcode, No UMI): smartseq</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>
@@ -90,9 +98,8 @@ 
</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): - 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>

<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, ICELL8, Smart-Seq, and STRT-Seq. For 10x Genomics, this is detected automatically but can be configured with the <code>--chemistry</code> argument. For other technologies, the template switching oligonucleotide is automatically converted to the match the 10x sequence.</p>

<p>Single indexes are supported for STRT-Seq, Quartz-Seq, and RamDA-Seq. Dual indexes are supported for inDrops-v3, SCI-RNA-Seq, scifi-seq, and Smart-Seq. Combinatorial indexing technologies have linkers between barcodes removed automatically to match the barcode whitelist.</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;\
@@ -103,6 +110,7 @@ 
<p>Custom inputs are also supported by giving the name &quot;custom&quot; 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>

<p>Custom barcode files are also supported for preset technologies. These are particularly useful for well-based technologies to demutliplex based on the wells.</p>

<p>Note that custom inputs do not remove linker or adapter sequences for combinatorial indexng technologies. These must be removed from the Read 1 file before running UniverSC. To request a preset technology setting instead, please submit a feature request on GitHub as described below.</p>

<h2 id="release">Release</h2>

<p>This tool will be released open-source (see <a href="#licensing">legal stuff</a> below). We welcome any feedback on it and any contributions to improve it. Hopefully it will save people time by making it easier to compare technologies.</p>

<p>We have tested it on several technologies but we need users like you to let us know how we can improve it. We hope that it will save you time by handing tedious parts of data formatting so that you can focus on the results.</p>
@@ -495,22 +503,27 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

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

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

                                  Drop-Seq (12 bp barcode, 8 bp UMI): nadia, dropseq

                                  Drop-Seq (12 bp barcode, 8 bp UMI): dropseq

                                  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

                                  ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom

                                  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

                                  Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq

                                  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

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

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

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

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

                                  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 (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq

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

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

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

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

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

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

                                  STRT-Seq (6 bp barcode, no UMI)

README.md

+33 −18
Original line number Diff line number Diff line
@@ -168,7 +168,9 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  CEL-Seq

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

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

-  Drop-Seq (12 bp barcode, 8 bp UMI): nadia, dropseq

-  Drop-Seq (12 bp barcode, 8 bp UMI): dropseq

-  ICELL8

    -  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

    -  ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom

-  inDrops

    -  inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1
@@ -178,10 +180,13 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
    -  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

-  Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq

-  Quartz-Seq

    -  QuartzSeq (6 bp index, no UMI): 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

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

-  Single-cell combinatorial indexing (SCI-RNA-Seq)

   -  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
@@ -189,8 +194,9 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3

-  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

   -  Smart-Seq (16 bp barcode, No UMI): smartseq

   -  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)
@@ -199,17 +205,17 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 


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.



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



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



is only supported for 10x Genomics version 2 chemistry, ICELL8, 

Smart-Seq, and STRT-Seq.

For 10x Genomics, this is detected automatically but can be

configured with the `--chemistry` argument.

For other technologies, the template switching oligonucleotide

is automatically converted to the match the 10x sequence. 



Single indexes are supported for STRT-Seq, Quartz-Seq, and RamDA-Seq.

Dual indexes are supported for inDrops-v3, SCI-RNA-Seq, scifi-seq, and Smart-Seq.

Combinatorial indexing technologies have linkers between barcodes removed

automatically to match the barcode whitelist.



#### Dual-indexing
@@ -232,6 +238,10 @@ Custom inputs are also supported by giving the name "custom" and length of barco 
Custom barcode files are also supported for preset technologies. These are particularly useful for well-based

technologies to demutliplex based on the wells.



Note that custom inputs do not remove linker or adapter sequences for combinatorial indexng technologies.

These must be removed from the Read 1 file before running UniverSC. To request a preset technology

setting instead, please submit a feature request on GitHub as described below.



## Release



This tool will be released open-source (see [legal stuff](#licensing) below).
@@ -1012,22 +1022,27 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

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

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

                                  Drop-Seq (12 bp barcode, 8 bp UMI): nadia, dropseq

                                  Drop-Seq (12 bp barcode, 8 bp UMI): dropseq

                                  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

                                  ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom

                                  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

                                  Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq

                                  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

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

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

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

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

                                  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 (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq

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

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

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

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

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

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

                                  STRT-Seq (6 bp barcode, no UMI)

launch_universc.sh

+8 −9
Original line number Diff line number Diff line
@@ -200,22 +200,27 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody

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

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

                                  Drop-Seq (12 bp barcode, 8 bp UMI): nadia, dropseq

                                  Drop-Seq (12 bp barcode, 8 bp UMI): dropseq

                                  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

                                  ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom

                                  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

                                  Nadia (12 bp barcode, 8 bp UMI): nadia, dropseq

                                  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

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

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

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

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

                                  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 (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq

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

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

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

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

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

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

                                  STRT-Seq (6 bp barcode, no UMI)
@@ -225,12 +230,6 @@ Mandatory arguments to long options are mandatory for short options too. 
                                Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_"

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



                                Experimental

                                  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)

  

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

man/launch_universc.sh

+8 −9

File changed.

Preview size limit exceeded, changes collapsed.

CRA Git | Maintained and supported by SUSTech CRA and CCSE