Commit 3cd4b4f4 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

remove separate subroutine for SPLIT-Seq (same as SLIPT-Seq2)

parent ec4df135

README.Rmd

+10 −5
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@@ -188,11 +188,17 @@ 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

-  Sci-Seq (8bp UMI, 30bp barcode): sciseq

-  SPLiT-Seq (10bp UMI, 18bp barcode): splitseq

-  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)



#### Dual-indexing
@@ -1009,8 +1015,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  SeqWell (12bp barcode, 8bp UMI): seqwell

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

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

                                  SPLiT-Seq (10bp UMI, 18bp barcode): splitseq

                                  SPLiT-Seq2 (10bp UMI, 24bp barcode): splitseq2

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

                                  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

README.html

+2 −3
Original line number Diff line number Diff line
@@ -67,7 +67,7 @@ 
</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): - inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 - Sci-Seq (8bp UMI, 30bp barcode): sciseq - SPLiT-Seq (10bp UMI, 18bp barcode): splitseq - SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad</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>

<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;\
@@ -484,8 +484,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  SeqWell (12bp barcode, 8bp UMI): seqwell

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

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

                                  SPLiT-Seq (10bp UMI, 18bp barcode): splitseq

                                  SPLiT-Seq2 (10bp UMI, 24bp barcode): splitseq2

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

                                  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

README.md

+11 −6
Original line number Diff line number Diff line
@@ -6,7 +6,7 @@ affiliations: 
   index: 1

 - name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan"

   index: 2

date: "Thursday 22 April 2021"

date: "Saturday 24 April 2021"

output:

  prettydoc::html_pretty:

       theme: cayman
@@ -188,11 +188,17 @@ 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

-  Sci-Seq (8bp UMI, 30bp barcode): sciseq

-  SPLiT-Seq (10bp UMI, 18bp barcode): splitseq

-  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)



#### Dual-indexing
@@ -1009,8 +1015,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  SeqWell (12bp barcode, 8bp UMI): seqwell

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

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

                                  SPLiT-Seq (10bp UMI, 18bp barcode): splitseq

                                  SPLiT-Seq2 (10bp UMI, 24bp barcode): splitseq2

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

                                  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

launch_universc.sh

+5 −33
Original line number Diff line number Diff line
@@ -214,8 +214,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  SeqWell (12bp barcode, 8bp UMI): seqwell

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

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

                                  SPLiT-Seq (10bp UMI, 18bp barcode): splitseq

                                  SPLiT-Seq2 (10bp UMI, 24bp barcode): splitseq2

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

                                  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
@@ -647,7 +646,7 @@ elif [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "smart-seq3" ]]; 
elif [[ "$technology" == "splitseq" ]] || [[ "$technology" == "split-seq" ]]; then

    technology="splitseq"

elif [[ "$technology" == "splitseq2" ]] || [[ "$technology" == "split-seq2" ]] || [[ "$technology" == "splitseq-v2" ]] || [[ "$technology" == "split-seq-v2" ]]; then

    technology="splitseq2"

    technology="splitseq"

elif [[ "$technology" == "strt-seq" ]] || [[ "$technology" == "strt" ]] || [[ "$technology" == "strtseq" ]]; then

     technology="strt-seq"

elif [[ "$technology" == "strt-seq-c1" ]] || [[ "$technology" == "strt-seqc1" ]] || [[ "$technology" == "strtseqc1" ]] || [[ "$technology" == "strtseq-c1" ]]; then
@@ -790,10 +789,6 @@ elif [[ "$technology" == "smartseq3" ]]; then 
    umilength=8

    minlength=16

elif [[ "$technology" == "splitseq" ]]; then

    barcodelength=18

    umilength=10

    minlength=18

elif [[ "$technology" == "splitseq2" ]]; then

     barcodelength=24

     umilength=10

     minlength=24
@@ -1604,11 +1599,6 @@ else 
             if [[ ! -f ${whitelistdir}/splitseq_barcode.txt ]]; then

                 echo "  ...generating combination of I1, I2, and RT barcodes..."

             fi

    elif [[ "$technology" == "splitseq2" ]]; then

             barcodefile=${whitelistdir}/splitseq2_barcode.txt

             if [[ ! -f ${whitelistdir}/splitseq2_barcode.txt ]]; then

                 echo "  ...generating combination of I1, I2, and RT barcodes..."

             fi

    elif [[ "$technology" == "smartseq3" ]]; then

        barcodefile=${whitelistdir}/SmartSeq3_barcode.txt

    elif [[ "$technology" == "strt-seq" ]]; then
@@ -1684,14 +1674,11 @@ else 
                 > ${whitelistdir}/sciseq3_barcode.txt

                 ## to filter unique lines: awk '!a[$0]++'  > ${whitelistdir}/sciseq3_barcode.txt

             fi

        elif [[ "$technology" == "splitseq" ]] || [[ "$technology" == "splitseq2" ]]; then

        elif [[ "$technology" == "splitseq" ]]; then

             #generates all combinations of I1-I2-R1 barcodes

             if [[ ! -f ${whitelistdir}/splitseq2_barcode.txt ]]; then

                 join -j 9999 ${whitelistdir}/split-seq2_round1_barcode.txt ${whitelistdir}/split-seq2_round2_barcode.txt | sed "s/ //g" | \

                 join -j 9999 - ${whitelistdir}/split-seq2_round3_barcode.txt | sed "s/ //g" | awk '!a[$0]++'  > ${whitelistdir}/splitseq2_barcode.txt

             fi

             if [[ ! -f ${whitelistdir}/splitseq_barcode.txt ]]; then

                 cp ${whitelistdir}/splitseq2_barcode.txt ${whitelistdir}/splitseq_barcode.txt

                 join -j 9999 ${whitelistdir}/split-seq_round1_barcode.txt ${whitelistdir}/split-seq_round2_barcode.txt | sed "s/ //g" | \

                 join -j 9999 - ${whitelistdir}/split-seq_round3_barcode.txt | sed "s/ //g" | awk '!a[$0]++'  > ${whitelistdir}/splitseq_barcode.txt

             fi

        elif [[ "$technology" == "strt-seq-2i" ]]; then

             if [[ ! -f ${whitelistdir}/STRTSeq2i_barcode.txt ]]; then
@@ -2678,21 +2665,6 @@ else 
    ## https://github.com/hms-dbmi/dropEst/issues/80

    ## https://github.com/sdparekh/zUMIs/wiki/Protocol-specific-setup

    if [[ "$technology" == "splitseq" ]]; then

        echo "  ...remove adapter and phase blocks for ${technology}"

        for convFile in "${convFiles[@]}"; do

            #remove phase blocks and linkers (swap barcode and UMI)

            sed -E '

                /^([ATCGA]{92})/ {

                s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})*/\2\3\4\1/g

                n

                n

                s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})*/\2\3\4\1/g

                }' $convFile > ${crIN}/.temp

            mv ${crIN}/.temp $convFile

        echo "  ...barcode and UMI swapped for ${technology}" #performed by \1 above

        done

    fi

    if [[ "$technology" == "splitseq2" ]]; then

        echo "  ...remove adapter and phase blocks for ${technology}"

        for convFile in "${convFiles[@]}"; do

            #remove phase blocks and linkers

man/launch_universc.sh

+1 −2
Original line number Diff line number Diff line
@@ -204,8 +204,7 @@ Provides a conversion script to run multiple technologies and custom libraries w 
                                  SeqWell (12bp barcode, 8bp UMI): seqwell

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

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

                                  SPLiT-Seq (10bp UMI, 18bp barcode): splitseq

                                  SPLiT-Seq2 (10bp UMI, 24bp barcode): splitseq2

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

                                  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

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