benchmarking SmartSeq subroutines

            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/' )

start=$(date +%s.%N)

            # reads matching adapter sequence for R1

            grep -A 2 -B 1 ATTGCGCAATG $convR1  | sed '/--/d' > ${convR1}.umi.fastq

            #match R2 to R1 containing UMI

            fastq_pair  ${convR1}.umi.fastq $convR2

end=$(date +%s.%N)

runtime=$(python -c "print(${end} - ${start})")

echo "Runtime for filtering with grep was $runtime"

            # uses bbduk (decontamination using k=mers) from BBMap(BBTools) vesion 38.87

            # step 1: process as paired ends to match k-mers (adapters matched are filtered)

            # step 1: process as paired ends to match k-mers (adapters matched are filtered) (clean = internal; fail = 5' UMI reads)

start1=$(date +%s.%N)

            bbduk.sh in1=${convR1}.umi.fastq.paired.fq in2=${convR2}.paired.fq outu1=$crIN/clean_R1.fq outu2=$crIN/clean_R2.fq outm1=$crIN/fail_R2.fq outm2=$crIN/fail_R1.fq outs=$crIN/pass_singletons.fq literal=ATTGCGCAATG k=10

end1=$(date +%s.%N)

runtime=$(python -c "print(${end1} - ${start1})")

echo "Runtime for filtering with bbduk.sh was $runtime"

            # step 2: take matched (adapter filtered) reads and remove adapter (and all bases to the left)

start2=$(date +%s.%N)

            bbduk.sh in1=$crIN/fail_R1.fq in2=$crIN/fail_R2.fq out1=$crIN/trimmed_R1.fq out2=$crIN/trimmed_R2.fq literal=ATTGCGCAATG ktrim=l k=11

            # match indexes to R1

            fastq_pair  ${convR1}.umi.fastq ${convI1}

            fastq_pair  ${convR1}.umi.fastq ${convI2}

end2=$(date +%s.%N)

runtime=$(python -c "print(${end2} - ${start2})")

echo "Runtime for trimming with bbduk.sh was $runtime"

runtime=$(python -c "print(${end2} - ${start1})")

echo "Runtime for trimming and filtering with bbduk.sh was $runtime"

            #replace original files

            mv ${convI1}.fastq.paired.fq ${convI1}

            mv ${convI2}.fastq.paired.fq ${convI2}

            rm $crIN/*fastq.paired.fq $crIN/*fastq.single.fq $crIN/clean_R1.fq $crIN/clean_R2.fq $crIN/fail_R1.fq $crIN/fail_R2.fq $crIN/pass_singletons.fq ${convR1}.umi.fastq

        done

    fi

exit 0

    #converting barcodes

    echo " adjusting barcodes of R1 files"

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