Commit ba171f73 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update split-seq2 parameters

parent 98062a04

README.Rmd

+1 −0
Original line number Diff line number Diff line
@@ -1010,6 +1010,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  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

                                  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

+1 −0
Original line number Diff line number Diff line
@@ -485,6 +485,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  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

                                  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.md

+1 −0
Original line number Diff line number Diff line
@@ -1010,6 +1010,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  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

                                  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

+10 −3
Original line number Diff line number Diff line
@@ -215,6 +215,7 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  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

                                  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
@@ -633,6 +634,8 @@ elif [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "smart-seq3" ]]; 
    nonUMI=false

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"

elif [[ "$technology" == "surecell" ]] || [[ "$technology" == "surecellseq" ]] || [[ "$technology" == "surecell-seq" ]] || [[ "$technology" == "ddseq" ]] || [[ "$technology" == "dd-seq" ]] || [[ "$technology" == "bioraad" ]]; then

    technology="surecell"

elif [[ "$technology" == "custom"* ]]; then
@@ -764,6 +767,10 @@ elif [[ "$technology" == "splitseq" ]]; then 
    barcodelength=18

    umilength=10

    minlength=18

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

     barcodelength=24

     umilength=10

     minlength=24

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

    barcodelength=18

    umilength=8
@@ -1378,7 +1385,7 @@ if [[ "$technology" == "indrop-v3" ]]; then 
fi



#inverting R1 and R2 for specific technologies

if [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "splitseq" ]]; then

if [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "splitseq2" ]]; then

    #invert read1 and read2

    echo "***WARNING: technology is set to ${technology}. barcodes on Read 2 will be used***"

    tmp=$read1
@@ -1479,7 +1486,7 @@ if [[ -n "$barcodefile" ]]; then 
        #getting absolute path

        barcodefile=$(readlink -f $barcodefile)

        #allowing WellList from ICELL8 and other well-based techniques

        if [[ "$technology" == "icell8" ]] || [[ "$technology" == "quartz-seq2*" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "smartseq*" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "custom" ]]; then

        if [[ "$technology" == "icell8" ]] || [[ "$technology" == "quartz-seq2*" ]] || [[ "$technology" == "splitseq" ]]|| [[ "$technology" == "splitseq2" ]] || [[ "$technology" == "smartseq*" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "custom" ]]; then

            seg=$'\t'

            n_col=$(awk -F'\t' '{print NF}' $barcodefile | sort -nu | tail -n 1)

            if [[ $n_col -eq 1 ]]; then
@@ -2481,7 +2488,7 @@ else 
    #SPLiT-Seq: correct phase blocks and swap barcode and UMI (if a whitelist and 18bp barcode can be supported)

    ## https://github.com/hms-dbmi/dropEst/issues/80

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

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

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

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

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

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

man/launch_universc.sh

+1 −0
Original line number Diff line number Diff line
@@ -205,6 +205,7 @@ Provides a conversion script to run multiple technologies and custom libraries w 
                                  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

                                  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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