Commit d6a994b4 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

correct inDrops-v3 specifications

parent bfe27a1f

README.Rmd

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@@ -118,8 +118,8 @@ avoid causing problems with existing runs). Multiple samples of the same technol 
-  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq

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

- inDrops

    -  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

    -  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

    -  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

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

-  Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
@@ -806,8 +806,8 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

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

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

                                  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

                                  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

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

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

README.html

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@@ -155,8 +155,8 @@ 
<li>ICELL8 version 3 (11bp barcode, 14bp UMI): icell8 or custom</li>

<li>inDrops

<ul>

<li>inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1</li>

<li>inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2</li>

<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>Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384</li>
@@ -576,8 +576,8 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

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

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

                                  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

                                  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

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

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

README.md

+4 −4
Original line number Diff line number Diff line
@@ -118,8 +118,8 @@ avoid causing problems with existing runs). Multiple samples of the same technol 
-  Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq

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

- inDrops

    -  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

    -  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

    -  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

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

-  Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
@@ -806,8 +806,8 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

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

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

                                  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

                                  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

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

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

launch_universc.sh

+3 −3
Original line number Diff line number Diff line
@@ -153,8 +153,8 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

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

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

                                  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

                                  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

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

                                  Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536
@@ -637,7 +637,7 @@ elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]]; t 
    umilength=6

    minlength=16

if [[ "$technology" == "indrop-v3" ]]; then

    barcodelength=8

    barcodelength=11

    umilength=6

    minlength=8

elif [[ "$technology" == "quartz-seq2-384" ]]; then

man/convert.sh

+2 −2
Original line number Diff line number Diff line
@@ -192,8 +192,8 @@ Provides a conversion script to run multiple technologies and custom libraries w 
                                  CEL-Seq2 (6bp UMI, 6bp barcode): celseq2

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

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

                                  inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2

                                  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

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

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

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