Commit 543d741e authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

correct index detection and chemistry parameters for SmartSeq2

parent bd0bcc9d

launch_universc.sh

+19 −16
Original line number Diff line number Diff line
@@ -1063,7 +1063,7 @@ if [[ $setup == "false" ]]; then 
                    R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' )

                    R4_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R4/' )

                    I1_file=$(echo $read | perl -pne 's/(.*)_R1/$1_I1/' )

                    if [[ -f $R4_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fq') ]]; then

                    if [[ -f $R4_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.gz' | head -n 1) ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fastq' | head -n 1) ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R4_file})'*.fq' | head -n 1) ]]; then

                        r4_present="true"

                        if [[ $verbose ]]; then

                            echo "  file $R4_file found, replacing $R1_file ..."
@@ -1081,7 +1081,7 @@ if [[ $setup == "false" ]]; then 
                        i1_read=$R2_file

                        i1_list[$j]=$i1_read

                    fi

                    if [[ -f $I1_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.fq') ]]; then

                    if [[ -f $I1_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.gz' | head -n 1) ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.fastq' | head -n 1) ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I1_file})'*.fq' | head -n 1) ]]; then

                        i1_present="true"

                        if [[ $verbose ]]; then

                            echo "  file $I1_file found ..."
@@ -1133,7 +1133,7 @@ if [[ $setup == "false" ]]; then 
                        R2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R2/' )

                        R3_file=$(echo $read | perl -pne 's/(.*)_R1/$1_R3/' )

                        I2_file=$(echo $read | perl -pne 's/(.*)_R1/$1_I2/' )

                        if [[ -f $R3_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.fq') ]]; then

                        if [[ -f $R3_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.gz' | head -n 1) ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.fastq' | head -n 1) ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${R3_file})'*.fq' | head -n 1) ]]; then

                            r3_present="true"

                            if [[ $verbose ]]; then

                                echo "  file $R3_file found, replacing $I2_file ..."
@@ -1146,7 +1146,7 @@ if [[ $setup == "false" ]]; then 
                                i2_list[$j]=$r3_read

                            fi

                        fi

                        if [[ -f $I2_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.gz') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.fastq') ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.fq') ]]; then

                        if [[ -f $I2_file ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.gz' | head -n 1) ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.fastq' | head -n 1) ]] || [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.fq' | head -n 1) ]]; then

                            i2_present="true"

                            if [[ $verbose ]]; then

                                echo "  file $I2_file found ..."
@@ -2160,7 +2160,7 @@ if [[ "$technology" == "10x" ]]; then 
        umiadjust=0

    fi

fi

if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "icell8-5-prime" ]]; then

if [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "icell8-5-prime" ]]; then

    if [[ $verbose ]]; then

        echo "  Using $chemistry for $technology"

    fi
@@ -3419,16 +3419,17 @@ else 
                }' $convR2 > ${crIN}/.temp

            mv ${crIN}/.temp $convR2

            

            echo " ... remove internal reads for ${technology} by matching TSO sequence for UMI reads"

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

            perl ${FILTERSMARTSEQREADUMI} --r1 ${convR1} --r2 ${convR2} --i1 ${convI1} --i2 ${convI2} --tag 'AAGCAGTGGTATCAACGCAGAGTAC' --out_dir ${crIN}

            echo "  ... trim tag sequence from R1"

#            echo " ... remove internal reads for ${technology} by matching TSO sequence for UMI reads"

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

#            perl ${FILTERSMARTSEQREADUMI} --r1 ${convR1} --r2 ${convR2} --i1 ${convI1} --i2 ${convI2} --tag 

'AAGCAGTGGTATCAACGCAGAGTAC' --out_dir ${crIN}

#            echo "  ... trim tag sequence from R1"

            

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

            mv $crIN/parsed_R1.fastq ${convR1}

            mv $crIN/parsed_R2.fastq ${convR2}

            mv $crIN/parsed_I1.fastq ${convI1}

            mv $crIN/parsed_I2.fastq ${convI2}

#            mv $crIN/parsed_R1.fastq ${convR1}

#            mv $crIN/parsed_R2.fastq ${convR2}

#            mv $crIN/parsed_I1.fastq ${convI1}

#            mv $crIN/parsed_I2.fastq ${convI2}

            

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

            #concatenate barcocdes from dual indexes to R1 as barcode (bases 1-16)
@@ -3442,7 +3443,6 @@ else 
            perl ${ADDMOCKUMI} --fastq ${convR1} --out_dir ${crIN} --head_length ${barcodelength} --umi_length ${umi_default}

            umilength=${umi_default}

            umiadjust=0

            chemistry="SC3Pv2"

            

            #returns a combined R1 file with barcode and mock UMI

            ##16 bp barcode, 10 bp UMI, GGG for TSO
@@ -3453,7 +3453,9 @@ else 
            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')

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

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



            if [[ $verbose ]]; then

                echo technology $technology

                echo barcode: $barcodelength
@@ -3464,7 +3466,8 @@ else 
            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')

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

            cmd=$(echo 'sed -E "4~4s/(.{'$barcodelength'})(.{'${umilength}'})/\1\2'$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

CRA Git | Maintained and supported by SUSTech CRA and CCSE