Commit 11d6de1c authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update dual index barcodes for SCI-Seq (2-level) to remove duplicate barcode whitelists

parent 58bf9a20

README.Rmd

+2 −2
Original line number Diff line number Diff line
@@ -189,7 +189,7 @@ We are developing technologies to support dual indexes and full length scRNA kit 


Experimental technologies (not yet supported):

-  inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

-  Sci-Seq (8bp UMI, 26bp barcode): sciseq

-  Sci-Seq (8bp UMI, 30bp barcode): sciseq

-  SPLiT-Seq (10bp UMI, 18bp barcode): splitseq

-  SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
@@ -1012,7 +1012,7 @@ Mandatory arguments to long options are mandatory for short options too. 


                                Experimental technologies (not yet supported):

                                  inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

                                  Sci-Seq (8bp UMI, 26bp barcode): sciseq

                                  Sci-Seq (8bp UMI, 30bp barcode): sciseq



  -b,  --barcodefile FILE       Custom barcode list in plain text (with each line containing a barcode)

README.html

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README.md

+2 −2
Original line number Diff line number Diff line
@@ -189,7 +189,7 @@ We are developing technologies to support dual indexes and full length scRNA kit 


Experimental technologies (not yet supported):

-  inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

-  Sci-Seq (8bp UMI, 26bp barcode): sciseq

-  Sci-Seq (8bp UMI, 30bp barcode): sciseq

-  SPLiT-Seq (10bp UMI, 18bp barcode): splitseq

-  SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad
@@ -1012,7 +1012,7 @@ Mandatory arguments to long options are mandatory for short options too. 


                                Experimental technologies (not yet supported):

                                  inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

                                  Sci-Seq (8bp UMI, 26bp barcode): sciseq

                                  Sci-Seq (8bp UMI, 30bp barcode): sciseq



  -b,  --barcodefile FILE       Custom barcode list in plain text (with each line containing a barcode)

launch_universc.sh

+10 −10
Original line number Diff line number Diff line
@@ -218,7 +218,7 @@ Mandatory arguments to long options are mandatory for short options too. 


                                Experimental technologies (not yet supported):

                                  inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

                                  Sci-Seq (8bp UMI, 26bp barcode): sciseq

                                  Sci-Seq (8bp UMI, 30bp barcode): sciseq



  -b,  --barcodefile FILE       Custom barcode list in plain text (with each line containing a barcode)
@@ -734,9 +734,9 @@ elif [[ "$technology" == "quartz-seq2-1536" ]]; then 
    umilength=8

    minlength=15

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

    barcodelength=26

    barcodelength=30

    umilength=8

    minlength=26

    minlength=30

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

    barcodelength=6 

    umilength=10
@@ -1583,7 +1583,7 @@ else 
            fi

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

             #generates all combinations of I1-I2-R1 barcodes

             join -j 9999 ${whitelistdir}/sci-seq3_i5_barcodes.txt ${whitelistdir}/sci-seq3_i7_barcodes.txt | join -j 9999 - ${whitelistdir}/sci-seq3_rt_barcodes.txt | sed "s/ //g"  > ${whitelistdir}/sciseq3_barcode.txt

             join -j 9999 ${whitelistdir}/sci-seq3_i5_barcodes.txt ${whitelistdir}/sci-seq3_i7_barcodes.txt | sed "s/ //g" | join -j 9999 - ${whitelistdir}/sci-seq3_rt_barcodes.txt | sed "s/ //g" | awk '!a[$0]++'  > ${whitelistdir}/sciseq3_barcode.txt

        else

            #generating permutations of ATCG of barcode length (non-standard evaluation required to run in script)

            echo $(eval echo $(for ii in $(eval echo {1..${barcodelength}}); do echo "{A,T,C,G}"; done | tr "\n" " " | sed "s/ //g" | xargs -I {} echo {})) | sed 's/ /\n/g' | sort | uniq > ${barcodefile}
@@ -1988,7 +1988,7 @@ if [[ $lock -eq 0 ]]; then 
    fi

    if [[ $old_rna_offset -gt 26 ]]; then

       if [[ $verbose ]]; then

           echo "RNA offset restored to 26 bp"

           echo "RNA offset restored to 30 bp"

       fi

       sed -i "s/'rna_read_offset': ${old_rna_offset},/'rna_read_offset': 26,/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py

       sed -i "s/'umi_read_length': ${old_umi_length},/'umi_read_length': 10,/g" ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/chemistry.py
@@ -2375,13 +2375,13 @@ else 
    if [[ "$technology" == "sciseq" ]]; then

        echo "  ...remove adapter for ${technology}"

        for convFile in "${convFiles[@]}"; do

            #remove adapter if detected

            #remove adapter if detected (and hairpin/tn5 barcode)

            sed -E '

                /^ACGACGCTCTTCCGATCT/ {

                s/^(.{18})//g

                /^ACGACGCTCTTCCGATCT(.{10})CAGAGC/ {

                s/^ACGACGCTCTTCCGATCT(.{10})CAGAGC(.{18})/\2/g

                n

                n

                s/^(.{18})//g

                s/^(.{26})(.{18})/\2/g

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

            mv ${crIN}/.temp $convFile

            #swap barcode and UMI
@@ -2396,7 +2396,7 @@ else 
            convI2=$(echo $read | perl -pne 's/(.*)_R1/$1_I2/' )



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

            # concatenate barcocdes from dual indexes to R1 as (bases 1-8 of the) barcode (bases 9-16), moving RT barcode (17-26) UMI to (27-35)

            # concatenate barcocdes from dual indexes to R1 as (bases 1-20 of the) barcode, moving RT barcode (21-30) UMI to (31-38)

            # 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

man/launch_universc.sh

+1 −1
Original line number Diff line number Diff line
@@ -208,7 +208,7 @@ Provides a conversion script to run multiple technologies and custom libraries w 


                                Experimental technologies (not yet supported):

                                  inDrops version 3 (16bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3

                                  Sci-Seq (8bp UMI, 26bp barcode): sciseq

                                  Sci-Seq (8bp UMI, 30bp barcode): sciseq



           A barcode whitelist is provided for all beads or wells for the following technologies:

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