Commit 03ba23dd authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

Merge branch 'master' of github.com:TomKellyGenetics/universc into stable

parents 63fab048 091572f4

launch_universc.sh

+68 −19
Original line number Diff line number Diff line
@@ -619,10 +619,15 @@ elif [[ "$technology" == "scrbseq" ]] || [[ "$technology" == "scrb-seq" ]] || [[ 
    technology="scrbseq"

elif [[ "$technology" == "seqwell" ]] || [[ "$technology" == "seq-well" ]]; then

    technology="seqwell"

elif [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smart-seq" ]] || [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smart-seq2" ]]

elif [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smart-seq" ]] || [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smart-seq2" ]]; then

    technology="smartseq2"

elif [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smart-seq2-umi" ]] ||  [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "smart-seq3" ]]; then

    technology="smartseq"

    nonUMI=true

elif [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smart-seq2-umi" ]]; then

    technology="smartseq2-umi"

    nonUMI=false

elif [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "smart-seq3" ]]; then

    technology="smartseq3"

    nonUMI=false

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

    technology="splitseq"

elif [[ "$technology" == "surecell" ]] || [[ "$technology" == "surecellseq" ]] || [[ "$technology" == "surecell-seq" ]] || [[ "$technology" == "ddseq" ]] || [[ "$technology" == "dd-seq" ]] || [[ "$technology" == "bioraad" ]]; then
@@ -813,6 +818,7 @@ elif [[ "$chemistry" != "$temp_chemistry" ]]; then 
    echo "***WARNING: chemistry is set to ${chemistry} where ${temp_chemistry} would have been chosen automatically. proceed with caution.***"

fi





#set default barcode and umi lengths

barcode_default=16

umi_default=10
@@ -931,7 +937,7 @@ fi 
#index 2

if [[ $setup == "false" ]]; then

    #only check I2 for dual-indexed techniques

    if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "smartseq" ]]; then

    if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "smartseq"* ]]; then

        if [[ ${#index2[@]} -ne ${#read1[@]} ]]; then

            if [[ ${#index2[@]} -gt 0 ]]; then

               echo " Error: number of index1 files is not matching the number of index2 files"
@@ -1609,10 +1615,13 @@ fi 
#allow "auto" only for 10x

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

    #use SC3Pv3 (umi length 12)

    if [[ $umilength -ge 11 ]] && [[ "$chemistry" == "SC3Pv1" ]] && [[ "$chemistry" == "SC3Pv2" ]]; then

    if [[ $umilength -ge 11 ]]; then

        if [[ "$chemistry" == "SC3Pv1" ]] || [[ "$chemistry" == "SC3Pv2" ]]; then

            echo "Using 10x version 3 chemistry to support longer UMIs"

            chemistry="SC3Pv3"

    else

            umi_default=12

        fi

    elif [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R1" ]] && [[ "$chemistry" != "SC5P-R2" ]] && [[ "$chemistry" != "fiveprime" ]]; then

        #use SC3Pv2 (umi length 10)

        echo "Using 10x version 2 chemistry to support UMIs"

        chemistry="SC3Pv2"
@@ -1623,10 +1632,13 @@ if [[ "$technology" != "10x" ]]; then 
    fi

fi

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

    if [[ $verbose ]]; then

        echo $chemistry

    fi

    if [[ "$chemistry" == "fiveprime" ]];  then

       chemistry="SC5P-PE"

    fi

    if [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R2" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then

    if [[ "$chemistry" != "SC5P-PE" ]] && [[ "$chemistry" != "SC5P-R1" ]] && [[ "$chemistry" != "SC5P-R2" ]]; then

        echo "Error: option --chemistry must be SC5P-PE, SC5P-R1 or SC5P-R2"

        exit

    fi
@@ -2380,6 +2392,28 @@ else 


            #returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)

            mv $crIN/Concatenated_File.fastq ${convR1}



            #convert TSO to expected length for 10x 5' (TSS in R1 from base 39)

            echo " handling $convFile ..."

            tsoS="TTTCTTATATGGG"

            tsoQ="IIIIIIIIIIIII"

            #Add 10x TSO characters to the end of the sequence

            cmd=$(echo 'sed -E "2~4s/(.{'$barcodelength'})(.{'${umilength}'})(.{3})/\1\2'$tsoS'/" '$convFile' > '${crIN}'/.temp')

            if [[ $verbose ]]; then

                echo technology $technology

                echo barcode: $barcodelength

                echo umi: $umilength

                echo $cmd

            fi

            # run command with barcode and umi length, e.g.,: sed -E "2~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoS\4/"  $convFile > ${crIN}/.temp

            eval $cmd

            mv ${crIN}/.temp $convFile

            #Add n characters to the end of the quality

            cmd=$(echo 'sed -E "4~4s/(.{'$barcodelength'})(.{'${umilength}'})(.{3})/\1\2'$tsoQ'/" '$convFile' > '${crIN}'/.temp')

            # run command with barcode and umi length, e.g.,: sed -E "4~4s/(.{16})(.{8})(.{3})(.*)/\1\2$tsoQ\4/"  $convFile > ${crIN}/.temp

            eval $cmd

            mv ${crIN}/.temp $convFile

            echo "  ${convFile} adjusted"

        done

    fi

    #Smart-Seq2
@@ -2409,17 +2443,32 @@ else 
    

    #UMI

    echo " adjusting UMIs of R1 files"

    # check if original UMI is shorter than default

    if [[ 0 -gt $umiadjust ]]; then

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

            echo " handling $convFile ..."

            toS=`printf '%0.sA' $(seq 1 $(($umiadjust * -1)))`

            toQ=`printf '%0.sI' $(seq 1 $(($umiadjust * -1)))`

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

            #compute length of adjusted barcode + original UMI

            keeplength=`echo $((${barcode_default}+${umi_default}-($umiadjust * -1)))`

                sed -i "2~2s/^\(.\{${keeplength}\}\).*/\1/" $convFile #Trim off everything beyond what is needed

            #Add n characters to the end of the sequence

            sed -E "2~4s/(.{$keeplength})(.*)/\1$toS\2/"  $convFile > ${crIN}/.temp

            mv ${crIN}/.temp $convFile

            #Add n characters to the end of the quality

            sed -E "4~4s/(.{$keeplength})(.*)/\1$toQ\2/"  $convFile > ${crIN}/.temp

            mv ${crIN}/.temp $convFile

            echo "  ${convFile} adjusted"

        done

    fi

            sed -i "2~4s/$/$toS/" $convFile #Add n characters to the end of the sequence

            sed -i "4~4s/$/$toQ/" $convFile #Add n characters to the end of the quality

    # check if original UMI is longer than default

    if [[ 0 -lt $umiadjust ]]; then

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

            echo " handling $convFile ..."

            #compute length of adjusted barcode + original UMI

            targetlength=`echo $((${barcode_default}+${umi_default}))`

            #Remove n characters to the end of the sequence and quality score

            sed -E "2~2s/(.{$targetlength})(.{$umiadjust})(.*)/\1\3/"  $convFile > ${crIN}/.temp

            mv ${crIN}/.temp $convFile

            echo "  ${convFile} adjusted"

        done

    fi

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