Commit e04d06e7 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

add inputs and barcode whitelists for ICELL8 5' scRNA (TCR) and SMART-Seq ICELL8 full-length scRNA

parent d7b33a8f

README.Rmd

+4 −0
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@@ -172,6 +172,8 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  ICELL8

    -  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

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

    -  ICELL8 5′ scRNA with TCR OR kit (10bp barcode, 8 bp UMI): icell8-5-prime

    -  ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length

-  inDrops

    -  inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1

    -  inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2
@@ -1058,6 +1060,8 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  Drop-Seq (12 bp barcode, 8 bp UMI): dropseq

                                  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

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

                                  ICELL8 5′ scRNA with TCR OR kit (10bp barcode, 8 bp UMI): icell8-5-prime

                                  ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length

                                  inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2

                                  inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3

README.html

+4 −0
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@@ -57,6 +57,8 @@ 
<ul>

<li>ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2</li>

<li>ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom</li>

<li>ICELL8 5′ scRNA with TCR OR kit (10bp barcode, 8 bp UMI): icell8-5-prime</li>

<li>ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length</li>

</ul></li>

<li>inDrops

<ul>
@@ -514,6 +516,8 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  Drop-Seq (12 bp barcode, 8 bp UMI): dropseq

                                  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

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

                                  ICELL8 5′ scRNA with TCR OR kit (10bp barcode, 8 bp UMI): icell8-5-prime

                                  ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length

                                  inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2

                                  inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3

README.md

+5 −1
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@@ -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: "Wednesday 28 April 2021"

date: "Thursday 06 May 2021"

output:

  prettydoc::html_pretty:

       theme: cayman
@@ -172,6 +172,8 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De 
-  ICELL8

    -  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

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

    -  ICELL8 5′ scRNA with TCR OR kit (10bp barcode, 8 bp UMI): icell8-5-prime

    -  ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length

-  inDrops

    -  inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1

    -  inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2
@@ -1058,6 +1060,8 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  Drop-Seq (12 bp barcode, 8 bp UMI): dropseq

                                  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

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

                                  ICELL8 5′ scRNA with TCR OR kit (10bp barcode, 8 bp UMI): icell8-5-prime

                                  ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length

                                  inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2

                                  inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3

launch_universc.sh

+47 −18
Original line number Diff line number Diff line
@@ -204,8 +204,10 @@ Mandatory arguments to long options are mandatory for short options too. 
                                  CEL-Seq (8 bp barcode, 4 bp UMI): celseq

                                  CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2

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

                                  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

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

                                  ICELL8 3′ scRNA version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

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

                                  ICELL8 5′ scRNA with TCR OR kit (10bp barcode, 8 bp UMI): icell8-5-prime

                                  ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length

                                  inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2

                                  inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3
@@ -633,9 +635,32 @@ elif [[ "$technology" == "nadia" ]] || [[ "$technology" == "dropseq" ]] || [[ "$ 
    technology="nadia"

elif [[ "$technology" == "icell8" ]] || [[ "$technology" == "icell-8" ]] ||  [[ "$technology" == "icell8-v3" ]] ||  [[ "$technology" == "icell8v3" ]]; then

    technology="icell8"

    #set as "icell8-5-prime" if called by chemistry

    if [[ "$chemistry" == "SC5P-"* ]] || [[ "$chemistry" == "fiveprime" ]]; then

        technology="icell8-icell8-5-prime"

        nonUMI=false

    fi

elif [[ "$technology" == "icell8-non-umi" ]] || [[ "$technology" == "icell8-nonumi" ]] ||  [[ "$technology" == "icell8-v2" ]] ||  [[ "$technology" == "icell8v2" ]]; then

    technology="icell8"

    nonUMI=true

elif [[ "$technology" == "icell8-five-prime" ]] || [[ "$technology" == "icell8fiveprime" ]] ||  [[ "$technology" == "icell8-5p" ]] ||  [[ "$technology" == "icell85p" ]]; then

    technology="icell8-5-prime"

    nonUMI=false

    if [[ -z ${chemistry} ]] || [[ ${chemistry} == "SC3Pv"* ]]; then

        if [[ $verbose ]]; then

            echo "setting chemistry for 5' scRNA"

        fi

        chemistry="SC5P-PE"

    fi

elif [[ "$technology" == "icell8-full" ]] || [[ "$technology" == "icell8-fl" ]] ||  [[ "$technology" == "icell8fl" ]] ||  [[ "$technology" == "smartseq-icell8" ]] || [[ "$technology" == "smart-seq-icell8" ]] || [[ "$technology" == "icell8-smart-seq" ]] || [[ "$technology" == "icell8smartseq" ]]; then

    technology="icell8-full-length"

    nonUMI=true

    if [[ -z ${chemistry} ]] || [[ ${chemistry} == "SC3Pv"* ]]; then

        if [[ $verbose ]]; then

            echo "setting chemistry for 5' scRNA"

        fi

        chemistry="SC5P-PE"

    fi

elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrops-v1" ]] || [[ "$technology" == "indropv1" ]] || [[ "$technology" == "indropsv1" ]] || [[ "$technology" == "1cellbio-v1" ]] || [[ "$technology" == "1cellbiov1" ]]; then

    technology="indrop-v1"

elif [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrops-v2" ]] || [[ "$technology" == "indropv2" ]] || [[ "$technology" == "indropsv2" ]] || [[ "$technology" == "1cellbio-v2" ]] || [[ "$technology" == "1cellbiov2" ]]; then
@@ -788,6 +813,10 @@ elif [[ "$technology" == "icell8" ]]; then 
       umilength=14

    fi

    minlength=11

elif [[ "$technology" == "icell8-5-prime" ]]; then

    barcodelength=10

    umilength=8

    minlength=10

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

    barcodelength=19

    umilength=6
@@ -808,18 +837,6 @@ elif [[ "$technology" == "marsseq-v2" ]]; then 
    barcodelength=7

    umilength=8

    minlength=7

elif [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]; then

     barcodelength=16

     if [[ $nonUMI ]]; then

         umilength=0

     fi

     minlength=16

elif [[ "$technology" == "quartz-seq" ]]; then

    barcodelength=6

    if [[ $nonUMI ]]; then

       umilength=0

    fi

    minlength=6

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

    barcodelength=14

    umilength=8
@@ -848,7 +865,7 @@ elif [[ "$technology" == "seqwell" ]]; then 
    barcodelength=8

    umilength=12

    minlength=8

elif [[ "$technology" == "smartseq2" ]] && [[ "$technology" == "smartseq3" ]]; then

elif [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "icell8-full-length" ]] || [[ "$technology" == "fluidigm-c1" ]] || [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "quartz-seq" ]] || [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]]; then

    barcodelength=16

    if [[ $nonUMI ]]; then

       umilength=0
@@ -1490,7 +1507,7 @@ fi 




#generate missing indexes if required (generating I1 and I2)

if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "smartseq2" ]] ||[[ "$technology" == "smartseq3" ]] || [[ "$technology" == "strt-seq-2i" ]] ; then

if [[ "$technology" == "indrop-v3" ]] ||  [[ "$technology" == "icell8-full-length" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "smartseq2" ]] ||[[ "$technology" == "smartseq3" ]] || [[ "$technology" == "strt-seq-2i" ]] ; then

     echo "dual indexes I1 and I2 required for $technology"

     if [[ ${#index2[@]} -le 1 ]]; then

         echo " automatically generating I1 and I2 index files from file headers"
@@ -1734,6 +1751,13 @@ else 
    elif [[ "$technology" == "icell8" ]]; then

        barcodefile=${whitelistdir}/ICELL8_barcode.txt

	echo "***WARNING: selected barcode file (${barcodefile}) contains barcodes for all wells in ICELL8. valid barcode will be an overestimate***"

    elif [[ "$technology" == "icell8-5-prime" ]]; then

        barcodefile=${whitelistdir}/ICELL8_TCR_barcode.txt

  elif [[ "$technology" == "icell8-full-length" ]]; then

        barcodefile=${whitelistdir}/SmartSeq_ICELL8_dual_barcodes.txt

        if [[ ! -f ${whitelistdir}/SmartSeq_ICELL8_dual_barcodes.txt ]]; then

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

        fi

    elif [[ "$technology" == "marsseq-v2" ]]; then

        barcodefile=${whitelistdir}/MARS-Seq2_barcode.txt

    elif [[ "$technology" == "microwellseq" ]]; then
@@ -1860,6 +1884,11 @@ else 
                #generates all combinations of I1-I2 barcodes

                join -j 9999 ${whitelistdir}/Illumina_Nextera_Index1_i7_barcodes.txt ${whitelistdir}/Illumina_Nextera_Index1_i5_barcodes.txt | sed "s/ //g" > ${whitelistdir}/Illumina_Nextera_dual_barcodes.txt

            fi

        elif [[ "$technology" == "icell8-full-length" ]]; then

            if [[ ! -f ${whitelistdir}/SmartSeq_ICELL8_dual_barcodes.txt ]]; then

                #generates all combinations of I1-I2 barcodes

                join -j 9999 ${whitelistdir}/ICELL8_full_length_Index1_i7_barcodes.txt ${whitelistdir}/ICELL8_full_length_Index2_i5_barcodes.txt |  sed "s/ //g" > ${whitelistdir}/SmartSeq_ICELL8_dual_barcodes.txt

            fi

        elif [[ "$technology" == "indrop-v"* ]]; then

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

                 perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v2 ${whitelistdir}
@@ -1991,7 +2020,7 @@ if [[ "$technology" != "10x" ]]; then 
       exit 1

    fi

fi

if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smartseq3" ]]; then

if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "icell8-5-prime" ]]; then

    if [[ $verbose ]]; then

        echo $chemistry

    fi
@@ -2651,7 +2680,7 @@ else 
    fi

    

    #C1, Quartz-Seq and RamDA-Seq: add mock UMI for non-UMI techniques

    elif [[ "$technology" == "fluidigm-c1" ]] || [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]] || [[ "$technology" == "quartz-seq" ]]; then

    elif [[ "$technology" == "fluidigm-c1" ]] || [[ "$technology" == "icell8-full-length" ]] || [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]] || [[ "$technology" == "quartz-seq" ]]; then

        echo "  ...processsing for ${technology}"

        if [[ $verbose ]]; then

            echo "Note: ${technology} does not contain UMIs"

man/launch_universc.sh

+2 −0
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@@ -203,6 +203,8 @@ Provides a conversion script to run multiple technologies and custom libraries w 
                                  Drop-Seq (12 bp barcode, 8 bp UMI): dropseq

                                  ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2

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

                                  ICELL8 5′ scRNA with TCR OR kit (10bp barcode, 8 bp UMI): icell8-5-prime

                                  ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length

                                  inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1

                                  inDrops version 2 (19 bp barcode, 6 bp UMI): indrops-v2, 1cellbio-v2

                                  inDrops version 3 (16 bp barcode, 6 bp UMI): indrops-v3, 1cellbio-v3

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