Loading launch_universc.sh +40 −11 Original line number Diff line number Diff line Loading @@ -644,8 +644,8 @@ elif [[ "$technology" == "quartz-seq2-384" ]] || [[ "$technology" == "quartzseq2 technology="quartz-seq2-384" elif [[ "$technology" == "quartz-seq2-1536" ]] || [[ "$technology" == "quartzseq2-1536" ]] || [[ "$technology" == "quartz-seq2-v3.2" ]] || [[ "$technology" == "quartzseq2-v3.2" ]] || [[ "$technology" == "quartzseq2v3.2" ]]; then technology="quartz-seq2-1536" elif [[ "$technology" == "rambda-seq" ]] || [[ "$technology" == "ram-da-seq" ]] || [[ "$technology" == "ramda-seq" ]]; then technology="rambda-seq" elif [[ "$technology" == "rambda-seq" ]] || [[ "$technology" == "lamda-seq" ]] || [[ "$technology" == "lambda-seq" ]] || [[ "$technology" == "ramdaseq" ]] || [[ "$technology" == "ram-da-seq" ]] || [[ "$technology" == "ramda-seq" ]]; then technology="ramda-seq" nonUMI=true elif [[ "$technology" == "sciseq" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "sci-rna-seq" ]]; then technology="sciseq3" Loading Loading @@ -760,7 +760,11 @@ elif [[ "$technology" == "nadia" ]]; then minlength=12 elif [[ "$technology" == "icell8" ]]; then barcodelength=11 if [[ $nonUMI ]]; then umilength=0 else umilength=14 fi minlength=11 elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]]; then barcodelength=19 Loading @@ -782,6 +786,12 @@ elif [[ "$technology" == "marsseq-v2" ]]; then barcodelength=7 umilength=8 minlength=7 elif [[ "$technology" == "quartz-seq" ]] && [[ "$technology" == "ramda-seq" ]]; then barcodelength=16 if [[ $nonUMI ]]; then umilength=0 fi minlength=16 elif [[ "$technology" == "quartz-seq2-384" ]]; then barcodelength=14 umilength=8 Loading Loading @@ -810,13 +820,13 @@ elif [[ "$technology" == "seqwell" ]]; then barcodelength=8 umilength=12 minlength=8 elif [[ "$technology" == "smartseq2" ]]; then barcodelength=16 umilength=8 minlength=16 elif [[ "$technology" == "smartseq3" ]]; then elif [[ "$technology" == "smartseq2" ]] && [[ "$technology" == "smartseq3" ]]; then barcodelength=16 if [[ $nonUMI ]]; then umilength=0 else umilength=8 fi minlength=16 elif [[ "$technology" == "splitseq" ]]; then barcodelength=24 Loading Loading @@ -1648,7 +1658,7 @@ 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-seq2*" ]] || [[ "$technology" == "microwellseq" ]] || [[ "$technology" == "smartseq*" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "splitseq2" ]] || [[ "$technology" == "custom" ]]; then if [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "icell8" ]] || [[ "$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" ]] || [[ "$technology" == "custom" ]]; then seg=$'\t' n_col=$(awk -F'\t' '{print NF}' $barcodefile | sort -nu | tail -n 1) if [[ $n_col -eq 1 ]]; then Loading Loading @@ -2723,6 +2733,25 @@ else done fi if [[ "$technology" == "quartz-seq" ]] && [[ "$technology" == "ramda-seq" ]]; then echo " ...processsing for ${technology}" if [[ $verbose ]]; then echo "Note: ICELL8 v2 does not contain UMIs" fi for convFile in "${convFiles[@]}"; do # add mock UMI (count reads instead of UMI) barcodelength=16, 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 ## 11 bp barcode, 10 bp UMI (TSO not handled yet) mv $crIN/mock_UMI.fastq ${convR1} done fi #QuartzSeq: remove adapter if [[ "$technology" == "quartz-seq2-384" ]]; then for convFile in "${convFiles[@]}"; do Loading Loading
launch_universc.sh +40 −11 Original line number Diff line number Diff line Loading @@ -644,8 +644,8 @@ elif [[ "$technology" == "quartz-seq2-384" ]] || [[ "$technology" == "quartzseq2 technology="quartz-seq2-384" elif [[ "$technology" == "quartz-seq2-1536" ]] || [[ "$technology" == "quartzseq2-1536" ]] || [[ "$technology" == "quartz-seq2-v3.2" ]] || [[ "$technology" == "quartzseq2-v3.2" ]] || [[ "$technology" == "quartzseq2v3.2" ]]; then technology="quartz-seq2-1536" elif [[ "$technology" == "rambda-seq" ]] || [[ "$technology" == "ram-da-seq" ]] || [[ "$technology" == "ramda-seq" ]]; then technology="rambda-seq" elif [[ "$technology" == "rambda-seq" ]] || [[ "$technology" == "lamda-seq" ]] || [[ "$technology" == "lambda-seq" ]] || [[ "$technology" == "ramdaseq" ]] || [[ "$technology" == "ram-da-seq" ]] || [[ "$technology" == "ramda-seq" ]]; then technology="ramda-seq" nonUMI=true elif [[ "$technology" == "sciseq" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "sci-rna-seq" ]]; then technology="sciseq3" Loading Loading @@ -760,7 +760,11 @@ elif [[ "$technology" == "nadia" ]]; then minlength=12 elif [[ "$technology" == "icell8" ]]; then barcodelength=11 if [[ $nonUMI ]]; then umilength=0 else umilength=14 fi minlength=11 elif [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]]; then barcodelength=19 Loading @@ -782,6 +786,12 @@ elif [[ "$technology" == "marsseq-v2" ]]; then barcodelength=7 umilength=8 minlength=7 elif [[ "$technology" == "quartz-seq" ]] && [[ "$technology" == "ramda-seq" ]]; then barcodelength=16 if [[ $nonUMI ]]; then umilength=0 fi minlength=16 elif [[ "$technology" == "quartz-seq2-384" ]]; then barcodelength=14 umilength=8 Loading Loading @@ -810,13 +820,13 @@ elif [[ "$technology" == "seqwell" ]]; then barcodelength=8 umilength=12 minlength=8 elif [[ "$technology" == "smartseq2" ]]; then barcodelength=16 umilength=8 minlength=16 elif [[ "$technology" == "smartseq3" ]]; then elif [[ "$technology" == "smartseq2" ]] && [[ "$technology" == "smartseq3" ]]; then barcodelength=16 if [[ $nonUMI ]]; then umilength=0 else umilength=8 fi minlength=16 elif [[ "$technology" == "splitseq" ]]; then barcodelength=24 Loading Loading @@ -1648,7 +1658,7 @@ 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-seq2*" ]] || [[ "$technology" == "microwellseq" ]] || [[ "$technology" == "smartseq*" ]] || [[ "$technology" == "seqwell" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "splitseq" ]] || [[ "$technology" == "splitseq2" ]] || [[ "$technology" == "custom" ]]; then if [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "icell8" ]] || [[ "$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" ]] || [[ "$technology" == "custom" ]]; then seg=$'\t' n_col=$(awk -F'\t' '{print NF}' $barcodefile | sort -nu | tail -n 1) if [[ $n_col -eq 1 ]]; then Loading Loading @@ -2723,6 +2733,25 @@ else done fi if [[ "$technology" == "quartz-seq" ]] && [[ "$technology" == "ramda-seq" ]]; then echo " ...processsing for ${technology}" if [[ $verbose ]]; then echo "Note: ICELL8 v2 does not contain UMIs" fi for convFile in "${convFiles[@]}"; do # add mock UMI (count reads instead of UMI) barcodelength=16, 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 ## 11 bp barcode, 10 bp UMI (TSO not handled yet) mv $crIN/mock_UMI.fastq ${convR1} done fi #QuartzSeq: remove adapter if [[ "$technology" == "quartz-seq2-384" ]]; then for convFile in "${convFiles[@]}"; do Loading
