replace inflated UMI for ICELL8 v2 (non-UMI) with mock to count reads

    fi

    #ICELL8 version 2 (non-UMI technology)

    if [[ "$technology" == "icell8" ]] && [[ $nonUMI ]];;then

    if [[ "$technology" == "icell8" ]] && [[ $nonUMI ]]; then

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

        if [[ $verbose ]]; then

            echo "Note: ICELL8 v2 does not contain UMIs"

            fi

            if [[ $nonUMI ]]; then

                #remove inflated umi (to replace with mock and count as reads)

                sed -E '

                    /^(.{11})(.{14})(.*)/ {

                    s/^(.{11})(.{14})(.*)/\1\3/g

                    n

                    n

                    s/^(.{11})(.{14})(.*)/\1\3/g

                    }' $convFile > ${crIN}/.temp

                mv ${crIN}/.temp $convFile

                # add mock UMI (count reads instead of UMI) barcodelength=16, 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

                ## 16 bp barcode, 10 bp UMI, GGG for TSO

                mv $crIN/mock_UMI.fastq ${convR1}

            fi

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

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