Commit 65876a79 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

add support for inDrops version 1 and 2

parent 5b026931

inDrops_barcodes.txt

+147456 −147456

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inDrops_barcodes_full.txt

+147456 −147456

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launch_universc.sh

+51 −17
Original line number Diff line number Diff line
@@ -72,12 +72,14 @@ Mandatory arguments to long options are mandatory for short options too. 
  -t,  --technology PLATFORM    Name of technology used to generate data.

                                Supported technologies:

                                  10x Genomics (16bp barcode, 10bp UMI): 10x, chromium (v2 or v3 automatically detected)

                                  CEL-Seq (6bp barcode, 6bp UMI): celseq

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

                                  iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom

                                  CEL-Seq (6bp barcode, 6bp UMI): celseq

                                  SCRUB-Seq (6bp barcode, 10bp UMI): scrubseq

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

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

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

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

                                  SCRUB-Seq (6bp barcode, 10bp UMI): scrubseq

                                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

  -b,  --barcodefile FILE       Custom barcode list in plain text (with each line containing a barcode)
@@ -439,10 +441,6 @@ if [[ "$technology" == "chromium" ]]; then 
    echo "Running with technology 10x (chromium)" 

    technology="10x"

fi

if [[ "$technology" == "dropseq" ]] || [[ "$technology" == "drop-seq" ]]; then

    echo "Running with Nadia parameters (Drop-Seq)"

    technology="nadia"

fi

if [[ "$technology" == "celseq" ]] || [[ "$technology" == "cel-seq" ]]; then

    echo "Running with CEL-Seq parameters (version 1)"

    technology="celseq"
@@ -451,11 +449,27 @@ if [[ "$technology" == "celseq2" ]] || [[ "$technology" == "cel-seq2" ]]; then 
    echo "Running with CEL-Seq2 parameters"

    technology="celseq2"

fi

if [[ "$technology" == "scrubseq" ]] || [[ "$technology" == "scrub-seq" ]]; then

    echo "Running with SCRUB-Seq parameters"

    technology="scrubseq"

if [[ "$technology" == "dropseq" ]] || [[ "$technology" == "drop-seq" ]]; then

    echo "Running with Nadia parameters (Drop-Seq)"

    technology="nadia"

fi

if [[ "$technology" == "icell8" ]] || [[ "$technology" == "icell-8" ]]; then

    echo "Running with iCELL8 parameters (version 3 with UMIs)"

    technology="icell8"

fi

if [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrops-v1" ]] || [[ "$technology" == "indropv1" ]] || [[ "$technology" == "indropsv1" ]]; then

    echo "Running with inDrop parameters (version 1)"

    technology="indrop-v1"

fi

if [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrops-v2" ]] || [[ "$technology" == "indropv2" ]] || [[ "$technology" == "indropsv2" ]]; then

    echo "Running with inDrop parameters (version 2 with reads inverted)"

    technology="indrop-v2"    

    #invert read1 and read2

    tmp=$read1 

    read1=$read2

    read2=$tmp  

    tmp=""

fi



if [[ "$technology" == "quartz-seq2-384" ]] || [[ "$technology" == "quartzseq2-384" ]] || [[ "$technology" == "quartz-seq2-v3.1" ]] || [[ "$technology" == "quartzseq2-v3.1" ]] || [[ "$technology" == "quartzseq2v3.1" ]]; then

    echo "Running with Quartz-Seq2 v3.1 parameters 384 wells (14bp barcode)"

    technology="quartz-seq2-384"
@@ -465,9 +479,14 @@ if [[ "$technology" == "quartz-seq2-1536" ]] || [[ "$technology" == "quartzseq2- 
    echo "Running with Quartz-Seq2 v3.2 parameters 1536 wells (15bp barcode)"

    technology="quartz-seq2-1536"

fi

if [[ "$technology" == "scrubseq" ]] || [[ "$technology" == "scrub-seq" ]]; then

    echo "Running with SCRUB-Seq parameters"

    technology="scrubseq"

fi





#check if technology matches expected inputs

if [[ "$technology" != "10x" ]] && [[ "$technology" != "nadia" ]] && [[ "$technology" != "icell8" ]]; then

if [[ "$technology" != "10x" ]] && [[ "$technology" != "nadia" ]] && [[ "$technology" != "icell8" ]] && [[ "$technology" != "celseq" ]] && [[ "$technology" != "scrubseq" ]] && [[ "$technology" != "quartz-seq2"* ]] && [[ "$technology" != "indrop"* ]]; then

    if [[ "$technology" != "custom"* ]]; then

        echo "Error: option -t needs to be 10x, nadia, icell8, or custom_<barcode>_<UMI>"

        exit 1
@@ -712,6 +731,8 @@ else 
        fi

    elif [[ "$technology" == "icell8" ]]; then

        barcodefile=${SDIR}/iCell8_barcode.txt

    elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]]; then

        barcodefile=${SDIR}/inDrops_barcodes.txt

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

        barcodefile=${SDIR}/Quartz-Seq2-384_barcode.txt

    elif [[ "$technology" == "quartz-seq2-1536" ]]; then
@@ -830,24 +851,27 @@ umilength="" 
if [[ "$technology" == "10x" ]]; then

    barcodelength=16

    umilength=10

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

    barcodelength=6

    umilength=6

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

    barcodelength=12

    umilength=8

elif [[ "$technology" == "icell8" ]]; then

    barcodelength=11

    umilength=14

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

    barcodelength=6

    umilength=6

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

    barcodelength=6 

    umilength=10 

elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]]; then

    barcodelength=19 

    umilength=8

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

    barcodelength=14

    umilength=8

elif [[ "$technology" == "quartz-seq2-1536" ]]; then

    barcodelength=15

    umilength=8 

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

    barcodelength=6 

    umilength=10

else

    custom=`echo $technology | grep -o "_" | wc -l`

    custom=$(($custom+1))
@@ -1106,6 +1130,16 @@ else 
    echo "  barcodes: ${barcodeadjust}bps at its head"

    echo "  UMIs: ${umiadjust}bps at its tail" 

    

    #remove adapter from inDrops

    if [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]];

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

             sed -E '2~2s/(.{38}).{4}/\1/' $convFile > ${crIN}/.temp

             mv ${crIN}/.temp $convFile

             sed -E 's/(.{10}).{22}/\1/' $convFile > ${crIN}/.temp

             mv ${crIN}/.temp $convFile

        done

    fi



    #converting barcodes

    echo " adjusting barcodes of R1 files"

    if [[ $barcodeadjust != 0 ]]; then

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