support Smart-Seq3 UMI reads with dual indexes

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

            # filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters 

            perl sub/FilterSmartSeqReadUMI.pl --r1=${convR1} --r2=${convR2} --i1=${convI1} --i2=${convI2} --out $crIN

            perl sub/FilterSmartSeqReadUMI.pl --r1=${convR1} --r2=${convR2} --i1=${convI1} --i2=${convI2} --out_dir $crIN

            # returns R1 with tag sequence removed (left trim) starting with 8pbp UMI and corresponding reads for I1, I2, and R2

#            mv $crIN/SmartSeq3_parsed_R1.fastq ${convR1}

#            mv $crIN/SmartSeq3_parsed_R2.fastq ${convR2}

#            mv $crIN/SmartSeq3_parsed_I1.fastq ${convI1}

#            mv $crIN/SmartSeq3_parsed_I2.fastq ${convI2}

            mv $crIN/SmartSeq3_parsed_R1.fastq ${convR1}

            mv $crIN/SmartSeq3_parsed_R2.fastq ${convR2}

            mv $crIN/SmartSeq3_parsed_I1.fastq ${convI1}

            mv $crIN/SmartSeq3_parsed_I2.fastq ${convI2}

            # filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters 

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

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

            mv $crIN/Concatenated_File.fastq ${convR1}

        done

    fi

exit 0

    #converting barcodes

    echo " adjusting barcodes of R1 files"

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

use Getopt::Long;

#####SCRIPT DESCRIPTION#####

#Script "cat_fastq.pl" given a reference file, and a list of fastq files, concatenates all the additive sequences to add in front of each reference read.

#Script "ConcatenateDualIndexBarcodes.pl" given a reference file, and a list of fastq files, concatenates all the additive sequences to add in front of each reference read.

###########

#setting the default values.

my $ref_fastq = "";

my @additives = ();

my $concatenated_fastq = "cat.fastq";

my $concatenated_fastq = "Concatenated_File.fastq";

my $out_dir = "";

#making the options into external arguments.

use Getopt::Long;

#####SCRIPT DESCRIPTION#####

#Script "parse_fastq.pl" given a set of I1, I2, R1, and R2, trims and parses R1 and only keep the corresponding reads in the other files.

#Script "FilterSmartSeqReadUMI.pl" given a set of I1, I2, R1, and R2, trims and parses R1 and only keep the corresponding reads in the other files.

###########