Commit 2efa7307 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

add default indexes and subroutines for QuartzSeq TruSeq and C1 dual-indexed Nextera libraries

parent f37d8599

launch_universc.sh

+57 −3
Original line number Diff line number Diff line
@@ -619,8 +619,10 @@ elif [[ "$technology" == "10x-v3" ]] || [[ "$technology" == "chromium-v3" ]]; th 
    technology="10x-v3"

elif [[ "$technology" == "c1" ]] || [[ "$technology" == "c1-fluidigm" ]] || [[ "$technology" == "fluidigm" ]] || [[ "$technology" == "fluidigm-c1" ]]|| [[ "$technology" == "fluidigmc1" ]] ||  [[ "$technology" == "c1-rna-seq" ]]|| [[ "$technology" == "c1-mrna-seq" ]] ||  [[ "$technology" == "c1-rnaseq" ]]|| [[ "$technology" == "c1-scrna" ]]; then

    technology="fluidigm-c1"

      nonUMI=true

elif [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "c1cage" ]] || [[ "$technology" == "cage-c1" ]] || [[ "$technology" == "cagec1" ]]; then

    technology="c1-cage"

      nonUMI=true

elif [[ "$technology" == "celseq" ]] || [[ "$technology" == "cel-seq" ]]; then

    technology="celseq"

elif [[ "$technology" == "celseq2" ]] || [[ "$technology" == "cel-seq2" ]]; then
@@ -1685,7 +1687,7 @@ if [[ -n "$barcodefile" ]]; then 
        barcodefile=$(readlink -f $barcodefile)

        custombarcodes=true

        #allowing WellList from ICELL8 and other well-based techniques

        if [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "icell8" ]] || [[ "$technology" == "quartz-seq" ]] || [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "quartz-seq2*" ]] || [[ "$technology" == "microwellseq" ]] || [[ "$technology" == "smartseq*" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "splitseq2" ]] || [[ "$technology" == "custom" ]]; then

        if [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "fluidigm-c1" ]] || [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "icell8" ]] || [[ "$technology" == "quartz-seq" ]] || [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]] || [[ "$technology" == "quartz-seq2*" ]] || [[ "$technology" == "microwellseq" ]] || [[ "$technology" == "smartseq*" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "splitseq2" ]] || [[ "$technology" == "custom" ]]; then

            seg=$'\t'

            n_col=$(awk -F'\t' '{print NF}' $barcodefile | sort -nu | tail -n 1)

            if [[ $n_col -eq 1 ]]; then
@@ -1724,6 +1726,11 @@ else 
             if [[ ! -f ${whitelistdir}/bd_rhapsody_barcode.txt ]]; then

                 echo "  ...generating combination of I1, I2, and RT barcodes..."

             fi

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

             barcodefile=${whitelistdir}/Illumina_Nextera_dual_barcodes.txt

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

                 echo "  ...generating combination of I1 and I2 barcodes..."

             fi

    elif [[ "$technology" == "icell8" ]]; then

        barcodefile=${whitelistdir}/ICELL8_barcode.txt

	echo "***WARNING: selected barcode file (${barcodefile}) contains barcodes for all wells in ICELL8. valid barcode will be an overestimate***"
@@ -1734,6 +1741,8 @@ else 
             if [[ ! -f ${whitelistdir}/microwellseq_barcode.txt ]]; then

                 echo "  ...generating combination of I1, I2, and RT barcodes..."

             fi

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

        barcodefile=${whitelistdir}/Illumina_TruSeq_LT_Index1_i7_barcodes.txt

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

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

    elif [[ "$technology" == "quartz-seq2-1536" ]]; then
@@ -1824,6 +1833,11 @@ else 
                 join -j 9999 ${whitelistdir}/bd_rhapsody_cell_label_section1.txt ${whitelistdir}/bd_rhapsody_cell_label_section2.txt | sed "s/ //g" | \

                 join -j 9999 - ${whitelistdir}/bd_rhapsody_cell_label_section3.txt | sed "s/ //g"  > ${whitelistdir}/bd_rhapsody_barcode.txt

             fi

        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

            fi

        elif [[ "$technology" == "indrop-v"* ]]; then

            if [[ "$technology" == "indrop-v1" ]] || [[ $technology"" == "indrop-v2" ]]; then

                 perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v2 ${whitelistdir}
@@ -2614,6 +2628,46 @@ else 
        done

    fi

    

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

            

            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

            

            #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

    

    #ICELL8 version 2 (non-UMI technology)

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

        echo "  ...processsing for ${technology}"
@@ -2827,7 +2881,7 @@ else 
    fi

    

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

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

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

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

        if [[ $verbose ]]; then

            echo "Note: ${technology} does not contain UMIs"
@@ -2840,7 +2894,7 @@ else 
            convI1=$(echo $read | perl -pne 's/(.*)_R1/$1_I1/' )

            

            #detect index length

            indexlength=$(($(head $I1_file -n 2 | tail -n 1 | wc -c) -1))

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

            barcodelength=$indexlength

            

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

whitelists/Illumina_Nextera_Index1_i5_barcodes.txt

0 → 100644
+36 −0
Original line number Diff line number Diff line 
AAGGAGTA

AAGGCTAT

ACTGCATA

AGAGTAGA

CCTAGAGT

CGTCTAAT

CTAAGCCT

CTATTAAG

CTCTCTAT

GAGCCTTA

GCGTAAGA

GTAAGGAG

TAGATCGC

TATCCTCT

TCGACTAG

TCTCTCCG

TTATGCGA

TTCTAGCT

ACTCTAGG

AGAGGATA

AGCTAGAA

AGGCTTAG

ATAGAGAG

ATAGCCTT

ATTAGACG

CGGAGAGA

CTAGTCGA

CTCCTTAC

CTTAATAG

GCGATCTA

TAAGGCTC

TACTCCTT

TATGCAGT

TCGCATAA

TCTACTCT

TCTTACGC

whitelists/Illumina_Nextera_Index1_i7_barcodes.txt

0 → 100644
+26 −0
Original line number Diff line number Diff line 
TAAGGCGA

CGTACTAG

AGGCAGAA

TCCTGAGC

GGACTCCT

TAGGCATG

CTCTCTAC

CAGAGAGG

GCTACGCT

CGAGGCTG

AAGAGGCA

GTAGAGGA

GCTCATGA

ATCTCAGG

ACTCGCTA

GGAGCTAC

GCGTAGTA

CGGAGCCT

TACGCTGC

ATGCGCAG

TAGCGCTC

ACTGAGCG

CCTAAGAC

CGATCAGT

TGCAGCTA

TCGACGTC

whitelists/Illumina_TruSeq_Index1_i5_barcodes.txt

0 → 100644
+32 −0
Original line number Diff line number Diff line 
TGAACCTT

TGCTAAGT

TGTTCTCT

TAAGACAC

CTAATCGA

CTAGAACA

TAAGTTCC

TAGACCTA

TATAGCCT

ATAGAGGC

CCTATCCT

GGCTCTGA

AGGCGAAG

TAATCTTA

CAGGACGT

GTACTGAC

AAGGTTCA

ACTTAGCA

AGAGAACA

GTGTCTTA

TCGATTAG

TGTTCTAG

GGAACTTA

TAGGTCTA

AGGCTATA

GCCTCTAT

AGGATAGG

TCAGAGCC

CTTCGCCT

TAAGATTA

ACGTCCTG

GTCAGTAC

whitelists/Illumina_TruSeq_Index1_i7_barcodes.txt

0 → 100644
+24 −0
Original line number Diff line number Diff line 
ATCACGAC

ACAGTGGT

CAGATCCA

ACAAACGG

ACCCAGCA

AACCCCTC

CCCAACCT

CACCACAC

GAAACCCA

TGTGACCA

AGGGTCAA

AGGAGTGG

ATTACTCG

TCCGGAGA

CGCTCATT

GAGATTCC

ATTCAGAA

GAATTCGT

CTGAAGCT

TAATGCGC

CGGCTATG

TCCGCGAA

TCTCGCGC

AGCGATAG

CRA Git | Maintained and supported by SUSTech CRA and CCSE