Commit f93ce731 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update documentation

parent 7a86dcf4

README.Rmd

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@@ -199,15 +199,15 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
   -  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

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

-  Smart-seq

   -  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

    -  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)

    -  STRT-Seq (6 bp barcode, no UMI): strt-seq

    -  STRT-Seq-C1 (8 bp barode, 5 bp UMI): strt-seq-c1

    -  STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i

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



#### Chemistry settings available
@@ -1138,9 +1138,9 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  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)

                                  STRT-Seq-C1 (8 bp barode, 5 bp UMI)

                                  STRT-Seq-2i (13 bp barcode, 6 bp UMI)

                                  STRT-Seq (6 bp barcode, no UMI): strt-seq

                                  STRT-Seq-C1 (8 bp barode, 5 bp UMI): strt-seq-c1

                                  STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i

                                  SureCell (18 bp barcode, 8 bp 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 (16 bp barcode, 10 bp UMI): custom_16_10

README.html

+7 −7
Original line number Diff line number Diff line
@@ -94,16 +94,16 @@ 
<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>SPLiT-Seq (10 bp UMI, 24 bp barcode): splitseq</li>

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

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

<li>STRT-Seq-C1 (8 bp barode, 5 bp UMI): strt-seq-c1</li>

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

</ul></li>

<li>SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad</li>

</ul>
@@ -576,9 +576,9 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  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)

                                  STRT-Seq-C1 (8 bp barode, 5 bp UMI)

                                  STRT-Seq-2i (13 bp barcode, 6 bp UMI)

                                  STRT-Seq (6 bp barcode, no UMI): strt-seq

                                  STRT-Seq-C1 (8 bp barode, 5 bp UMI): strt-seq-c1

                                  STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i

                                  SureCell (18 bp barcode, 8 bp 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 (16 bp barcode, 10 bp UMI): custom_16_10

README.md

+7 −7
Original line number Diff line number Diff line
@@ -199,15 +199,15 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
   -  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

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

-  Smart-seq

   -  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

    -  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)

    -  STRT-Seq (6 bp barcode, no UMI): strt-seq

    -  STRT-Seq-C1 (8 bp barode, 5 bp UMI): strt-seq-c1

    -  STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i

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



#### Chemistry settings available
@@ -1138,9 +1138,9 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  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)

                                  STRT-Seq-C1 (8 bp barode, 5 bp UMI)

                                  STRT-Seq-2i (13 bp barcode, 6 bp UMI)

                                  STRT-Seq (6 bp barcode, no UMI): strt-seq

                                  STRT-Seq-C1 (8 bp barode, 5 bp UMI): strt-seq-c1

                                  STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i

                                  SureCell (18 bp barcode, 8 bp 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 (16 bp barcode, 10 bp UMI): custom_16_10

launch_universc.sh

+3 −3
Original line number Diff line number Diff line
@@ -229,9 +229,9 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  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)

                                  STRT-Seq-C1 (8 bp barode, 5 bp UMI)

                                  STRT-Seq-2i (13 bp barcode, 6 bp UMI)

                                  STRT-Seq (6 bp barcode, no UMI): strt-seq

                                  STRT-Seq-C1 (8 bp barode, 5 bp UMI): strt-seq-c1

                                  STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i

                                  SureCell (18 bp barcode, 8 bp 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 (16 bp barcode, 10 bp UMI): custom_16_10

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