Loading README.Rmd +2 −2 Original line number Diff line number Diff line Loading @@ -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, 22bp barcode): sciseq - Sci-Seq (8bp UMI, 26bp barcode): sciseq - SPLiT-Seq (10bp UMI, 18bp barcode): splitseq - SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad Loading Loading @@ -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, 22bp barcode): sciseq Sci-Seq (8bp UMI, 26bp barcode): sciseq -b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode) Loading README.html +0 −599 File changed.Preview size limit exceeded, changes collapsed. Show changes README.md +3 −3 Original line number Diff line number Diff line Loading @@ -6,7 +6,7 @@ affiliations: index: 1 - name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan" index: 2 date: "Thursday 04 March 2021" date: "Friday 16 April 2021" output: prettydoc::html_pretty: theme: cayman Loading Loading @@ -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, 22bp barcode): sciseq - Sci-Seq (8bp UMI, 26bp barcode): sciseq - SPLiT-Seq (10bp UMI, 18bp barcode): splitseq - SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad Loading Loading @@ -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, 22bp barcode): sciseq Sci-Seq (8bp UMI, 26bp barcode): sciseq -b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode) Loading launch_universc.sh +5 −5 Original line number Diff line number Diff line Loading @@ -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, 22bp barcode): sciseq Sci-Seq (8bp UMI, 26bp barcode): sciseq -b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode) Loading Loading @@ -734,9 +734,9 @@ elif [[ "$technology" == "quartz-seq2-1536" ]]; then umilength=8 minlength=15 elif [[ "$technology" == "sciseq" ]]; then barcodelength=22 barcodelength=26 umilength=8 minlength=22 minlength=26 elif [[ "$technology" == "scrbseq" ]]; then barcodelength=6 umilength=10 Loading Loading @@ -2366,7 +2366,7 @@ else convI2=$(echo $read | perl -pne 's/(.*)_R1/$1_I2/' ) echo " ...concatencate barcodes to R1 from I1 and I2 index files" # concatenate barcocdes from dual indexes to R1 as (bases 1-8 of the) barcode (bases 1-16), moving UMI to (17-22) # concatenate barcocdes from dual indexes to R1 as (bases 1-8 of the) barcode (bases 9-16), moving RT barcode (17-26) UMI to (27-35) # filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir $crIN Loading man/launch_universc.sh +1 −1 Original line number Diff line number Diff line Loading @@ -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, 22bp barcode): sciseq Sci-Seq (8bp UMI, 26bp barcode): sciseq A barcode whitelist is provided for all beads or wells for the following technologies: Loading Loading
README.Rmd +2 −2 Original line number Diff line number Diff line Loading @@ -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, 22bp barcode): sciseq - Sci-Seq (8bp UMI, 26bp barcode): sciseq - SPLiT-Seq (10bp UMI, 18bp barcode): splitseq - SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad Loading Loading @@ -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, 22bp barcode): sciseq Sci-Seq (8bp UMI, 26bp barcode): sciseq -b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode) Loading
README.md +3 −3 Original line number Diff line number Diff line Loading @@ -6,7 +6,7 @@ affiliations: index: 1 - name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan" index: 2 date: "Thursday 04 March 2021" date: "Friday 16 April 2021" output: prettydoc::html_pretty: theme: cayman Loading Loading @@ -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, 22bp barcode): sciseq - Sci-Seq (8bp UMI, 26bp barcode): sciseq - SPLiT-Seq (10bp UMI, 18bp barcode): splitseq - SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad Loading Loading @@ -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, 22bp barcode): sciseq Sci-Seq (8bp UMI, 26bp barcode): sciseq -b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode) Loading
launch_universc.sh +5 −5 Original line number Diff line number Diff line Loading @@ -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, 22bp barcode): sciseq Sci-Seq (8bp UMI, 26bp barcode): sciseq -b, --barcodefile FILE Custom barcode list in plain text (with each line containing a barcode) Loading Loading @@ -734,9 +734,9 @@ elif [[ "$technology" == "quartz-seq2-1536" ]]; then umilength=8 minlength=15 elif [[ "$technology" == "sciseq" ]]; then barcodelength=22 barcodelength=26 umilength=8 minlength=22 minlength=26 elif [[ "$technology" == "scrbseq" ]]; then barcodelength=6 umilength=10 Loading Loading @@ -2366,7 +2366,7 @@ else convI2=$(echo $read | perl -pne 's/(.*)_R1/$1_I2/' ) echo " ...concatencate barcodes to R1 from I1 and I2 index files" # concatenate barcocdes from dual indexes to R1 as (bases 1-8 of the) barcode (bases 1-16), moving UMI to (17-22) # concatenate barcocdes from dual indexes to R1 as (bases 1-8 of the) barcode (bases 9-16), moving RT barcode (17-26) UMI to (27-35) # filter UMI reads by matching tag sequence ATTGCGCAATG (bases 1-11 of R1) and remove as an adapters perl sub/ConcatenateDualIndexBarcodes.pl --additive=${convI1} --additive=${convI2} --ref_fastq=${convR1} --out_dir $crIN Loading
man/launch_universc.sh +1 −1 Original line number Diff line number Diff line Loading @@ -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, 22bp barcode): sciseq Sci-Seq (8bp UMI, 26bp barcode): sciseq A barcode whitelist is provided for all beads or wells for the following technologies: Loading
