Commit 7d18236f authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

automatic detection of barcode length from index files for C1, Quartz-Seq and RamDA-Seq 

and use TruSeq or Nextera indexes for Quartz-Seq
parent 2efa7307

launch_universc.sh

+42 −52
Original line number Diff line number Diff line
@@ -1742,7 +1742,26 @@ else 
                 echo "  ...generating combination of I1, I2, and RT barcodes..."

             fi

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

        indexlength=$(($(head $index1([0]) -n 2 | tail -n 1 | wc -c) -1))

        if [[ -f $index2([0]) ]]; then

            index2length=$(($(head $index2([0]) -n 2 | tail -n 1 | wc -c) -1))

            barcodelength=$(($indexlength + $index2length))

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

                cat ${whitelistdir}/Illumina_TruSeq_Index1_i7_barcodes.txt ${whitelistdir}/Illumina_Nextera_Index1_i7_barcodes.txt | sort | uniq > ${whitelistdir}/Illumina_Index1_i7_barcodes.txt

                cat ${whitelistdir}/Illumina_TruSeq_Index1_i5_barcodes.txt ${whitelistdir}/Illumina_Nextera_Index1_i5_barcodes.txt | sort | uniq > ${whitelistdir}/Illumina_Index1_i7_barcodes.txt

                join -j 9999 ${whitelistdir}/Illumina_Index1_i7_barcodes.txt ${whitelistdir}/Illumina_Index1_i5_barcodes.txt | sed "s/ //g" > ${whitelistdir}/Illumina_dual_barcodes.txt



            fi

            barcodefile=${whitelistdir}/Illumina_dual_barcodes.txt

        else

            barcodelength=$indexlength

            if [[ $indexlength -eq 6 ]]; then

                barcodefile=${whitelistdir}/Illumina_TruSeq_LT_Index1_i7_barcodes.txt

            else

                cat ${whitelistdir}/Illumina_TruSeq_Index1_i7_barcodes.txt ${whitelistdir}/Illumina_Nextera_Index1_i7_barcodes.txt >${whitelistdir}/Illumina_Index1_i7_barcodes.txt

                barcodefile=${whitelistdir}/Illumina_Nextera_Index1_i7_barcodes.txt

            fi

        fi

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

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

    elif [[ "$technology" == "quartz-seq2-1536" ]]; then
@@ -1836,7 +1855,7 @@ else 
        elif [[ "$technology" == "fluidigm-c1" ]] || [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]]; then

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

                #generates all combinations of I1-I2 barcodes

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

                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" == "indrop-v"* ]]; then

            if [[ "$technology" == "indrop-v1" ]] || [[ $technology"" == "indrop-v2" ]]; then
@@ -2628,27 +2647,37 @@ else 
        done

    fi

    

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

    #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

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

        if [[ $verbose ]]; then

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

        fi

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

            

            read=$convFile

            convR1=$read

            convR2=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' )

            convI1=$(echo $read | perl -pne 's/(.*)_R1/$1_I1/' )

            convI2=$(echo $read | perl -pne 's/(.*)_R1/$1_I2/' )

            

            #detect index length

            indexlength=$(($(head $convI1 -n 2 | tail -n 1 | wc -c) -1))

            index2length=$(($(head $convI2 -n 2 | tail -n 1 | wc -c) -1))

            barcodelength=$(($indexlength = $index2length))

            #detect barcode length from index sequence

            indexlength=$(($(head $index1([0]) -n 2 | tail -n 1 | wc -c) -1))

            barcodelength=$indexlength

            #detect whether index 2 files exist

            if [[ -f $index2([0]) ]]; then

                #detect barcode length from length of both index sequences

                index2length=$(($(head $index2([0]) -n 2 | tail -n 1 | wc -c) -1))

                barcodelength=$(($indexlength + $index2length))

                convI2=$(echo $read | perl -pne 's/(.*)_R1/$1_I2/' )

                

                echo "  ...concatencate barcodes to R1 from I1 and I2 index files"

                # concatenate barcocdes from index to R1 as (bases 1-16 of the) barcode, moving (read to start at base 17-)

                perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir $crIN

            else

                barcodelength=$indexlength

                echo "  ...concatencate barcodes to R1 from I1 index files"

                # concatenate barcocdes from index to R1 as (bases 1-6 of the) barcode, moving (read to start at base 7-)

            perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir $crIN

                perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --ref_fastq=${convR1} --out_dir $crIN

            fi

            

            #returns a combined R1 file with I1-R1 concatenated (I1 is cell barcode)

            mv $crIN/Concatenated_File.fastq ${convR1}
@@ -2880,45 +2909,6 @@ else 
        done

    fi

    

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

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

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

        if [[ $verbose ]]; then

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

        fi

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

            

            read=$convFile

            convR1=$read

            convR2=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' )

            convI1=$(echo $read | perl -pne 's/(.*)_R1/$1_I1/' )

            

            #detect index length

            indexlength=$(($(head $convI1 -n 2 | tail -n 1 | wc -c) -1))

            barcodelength=$indexlength

            

            echo "  ...concatencate barcodes to R1 from I1 index files"

            # concatenate barcocdes from index to R1 as (bases 1-6 of the) barcode, moving (read to start at base 7-)

            perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --ref_fastq=${convR1} --out_dir $crIN

            

            #returns a combined R1 file with I1-R1 concatenated (I1 is cell barcode)

            mv $crIN/Concatenated_File.fastq ${convR1}

            

            if [[ $nonUMI ]]; then

                # add mock UMI (count reads instead of UMI) barcodelength=6, umi_default=10

                perl sub/AddMockUMI.pl --fastq=${convR1} --out_dir $crIN --head_length=$barcodelength --umi_length=$umi_default

                umilength=$umi_default

                umiadjust=0

                if [[ $chemistry == "SC3Pv3" ]]; then

                    chemistry="SC3Pv2"

                fi

                #returns a combined R1 file with barcode and mock UMI

                ## 6 bp barcode, 10 bp UMI (TSO not handled yet)

                mv $crIN/mock_UMI.fastq ${convR1}

            fi

        done

    fi

    

    #Quartz-Seq2: remove adapter

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

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

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