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support BD Rhapsody v2 2022 enhanced beads
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  addresses issues #13 #14 #15
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@TomKellyGenetics
TomKellyGenetics committed May 25, 2023
1 parent 6106af3 commit ade8f8f
Showing 1 changed file with 24 additions and 6 deletions.
30 changes: 24 additions & 6 deletions launch_universc.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -228,7 +228,8 @@ Mandatory arguments to long options are mandatory for short options too.
10x Genomics version 2 (16 bp barcode, 10 bp UMI): 10x-v2, chromium-v2
10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3
Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo
BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody
BD Rhapsody v1 (27 bp barcode, 8 bp UMI): bd-rhapsody
BD Rhapsody v2 enhanced beads (27 bp barcode, 8 bp UMI): bd-rhapsody-v2
C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1
C1 CAGE (16 bp, No UMI): c1-cage
C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq
Expand Down Expand Up @@ -692,6 +693,8 @@ elif [[ "$technology" == "10x-v3" ]] || [[ "$technology" == "chromium-v3" ]]; th
technology="10x-v3"
elif [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "bd" ]] || [[ "$technology" == "rhapsody" ]] || [[ "$technology" == "bdrhapsody" ]]; then
technology="bd-rhapsody"
elif [[ "$technology" == "bd-rhapsody-v2" ]] || [[ "$technology" == "bd-v2" ]] || [[ "$technology" == "rhapsody-v2" ]] || [[ "$technology" == "bdrhapsody-v2" ]] || [[ "$technology" == "bd-rhapsodyv2" ]] || [[ "$technology" == "bdv2" ]] || [[ "$technology" == "rhapsodyv2" ]] || [[ "$technology" == "bdrhapsodyv2" ]] || [[ "$technology" == "bd-rhapsody-2022" ]] || [[ "$technology" == "bd-2022" ]] || [[ "$technology" == "rhapsody-2022" ]] || [[ "$technology" == "bdrhapsody-2022" ]] || [[ "$technology" == "bd-rhapsody2022" ]] || [[ "$technology" == "bd2022" ]] || [[ "$technology" == "rhapsody2022" ]] || [[ "$technology" == "bdrhapsody2022" ]]; then
technology="bd-rhapsody-v2"
elif [[ "$technology" == "aligent" ]] || [[ "$technology" == "bravo" ]] || [[ "$technology" == "aligent-bravo" ]] || [[ "$technology" == "bravo-b" ]] || [[ "$technology" == "aligent-bravo-b" ]]; then
techology="bravo"
nonUMI=false
Expand Down Expand Up @@ -864,7 +867,7 @@ elif [[ "$technology" == "10x-v3" ]]; then
minlength=16
chemistry="SC3Pv3"
technology="10x"
elif [[ "$technology" == "bd-rhapsody" ]]; then
elif [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "bd-rhapsody-v2" ]]; then
barcodelength=27
umilength=8
minlength=27
Expand Down Expand Up @@ -1880,7 +1883,7 @@ if [[ -n "$barcodefile" ]]; then
barcodefile=$(readlink -f $barcodefile)
custombarcodes=true
#allowing WellList from ICELL8 and other well-based techniques
if [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "bravo" ]] || [[ "$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" ]] || [[ "$technology" == "custom" ]]; then
if [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "bd-rhapsody-v2" ]] || [[ "$technology" == "bravo" ]] || [[ "$technology" == "fluidigm-c1" ]] || [[ "$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 [[ $n_col -eq 1 ]]; then
Expand Down Expand Up @@ -1914,7 +1917,7 @@ if [[ -n "$barcodefile" ]]; then
else
if [[ "$technology" == "10x"* ]]; then
barcodefile="default:10x"
elif [[ "$technology" == "bd-rhapsody" ]]; then
elif [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "bd-rhapsody-v2" ]]; then
barcodefile=${whitelistdir}/bd_rhapsody_barcode.txt
if [[ ! -f ${whitelistdir}/bd_rhapsody_barcode.txt ]]; then
echo " generating combination of I1, I2, and RT barcodes ..."
Expand Down Expand Up @@ -2052,7 +2055,7 @@ else
if [[ $verbose ]]; then
echo " generating a new barcode whitelist for ${technology}"
fi
if [[ "$technology" == "bd-rhapsody" ]]; then
if [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "bd-rhapsody-v2" ]]; then
if [[ ! -f ${whitelistdir}/bd_rhapsody_barcode.txt ]]; then
#generates all combinations of I1-I2-R1 barcodes
join -j 9999 ${whitelistdir}/bd_rhapsody_cell_label_section1.txt ${whitelistdir}/bd_rhapsody_cell_label_section2.txt | sed "s/ //g" | \
Expand Down Expand Up @@ -3015,7 +3018,22 @@ else
s/.*(.{9})ACTGGCCTGCGA(.{9})GGTAGCGGTGACA(.{9})(.{8})/\1\2\3\4/g
n
n
s/.*(.{6}).{12}(.{6}).{13}(.{6})(.{8})/\1\2\3\4/g
s/.*(.{9}).{12}(.{9}).{13}(.{9})(.{8})/\1\2\3\4/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
done
fi
#BD Rhapsody v2: remove adapters for enhanced beads (released in 2022)
if [[ "$technology" == "bd-rhapsody" ]]; then
echo " ... remove adapter and phase blocks for ${technology}"
for convFile in "${convFiles[@]}"; do
#remove phase blocks and linkers
sed -E '
/.*[ACG][CGT](.{9})GTGA(.{9})GACA(.{9})(.{8})/ {
s/.*(.{9})GTGA(.{9})GACA(.{9})(.{8})/\1\2\3\4/g
n
n
s/.*(.{9}).{4}(.{9}).{4}(.{9})(.{8})/\1\2\3\4/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
done
Expand Down

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