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configure barcode combinations and linker removal for Singleron GEXSC…
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…OPE versions 1-3 #17
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@TomKellyGenetics
TomKellyGenetics committed Feb 24, 2024
1 parent f686ffc commit ae4ce3b
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157 changes: 156 additions & 1 deletion launch_universc.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -2056,6 +2056,16 @@ else
if [[ ! -f ${whitelistdir}/Illumina_Nextera_dual_barcodes.txt ]]; then
echo " generating combination of I1 and I2 barcodes ..."
fi
elif [[ "$technology" == "gexscope-v2.0.0" ]] || [[ "$technology" == "gexscope-v2.0.1" ]] || [[ "$technology" == "gexscope-v2.1.0" ]] || [[ "$technology" == "gexscope-v2.1.1" ]] || [[ "$technology" == "gexscope-v2.2.0" ]] || [[ "$technology" == "gexscope-v2.2.1" ]]; then
barcodefile=${whitelistdir}/GEXSCOPE-v2_barcodes.txt
if [[ ! -f ${whitelistdir}/GEXSCOPE-v2_barcodes.txt ]]; then
echo " generating combination of 3 barcodes ..."
fi
elif [[ "$technology" == "gexscope-v3.0.0" ]] || [[ "$technology" == "gexscope-v3.0.1" ]]; then
barcodefile=${whitelistdir}/GEXSCOPE-v3_barcodes.txt
if [[ ! -f ${whitelistdir}/GEXSCOPE-v3_barcodes.txt ]]; then
echo " generating combination of 3 barcodes ..."
fi
elif [[ "$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***"
Expand Down Expand Up @@ -2241,6 +2251,22 @@ else
sort | uniq \
> ${whitelistdir}/Illumina_Nextera_dual_barcodes.txt
fi
elif [[ "$technology" == "gexscope-v2.0.0" ]] || [[ "$technology" == "gexscope-v2.0.1" ]] || [[ "$technology" == "gexscope-v2.1.0" ]] || [[ "$technology" == "gexscope-v2.1.1" ]] || [[ "$technology" == "gexscope-v2.2.0" ]] || [[ "$technology" == "gexscope-v2.2.1" ]]; then
if [[ ! -f ${whitelistdir}/GEXSCOPE-v2_barcodes.txt ]]; then
#generates all combinations of R2 barcodes
join -j 9999 ${whitelistdir}/bc_gexscope_v2.txt ${whitelistdir}/bc_gexscope_v2..txt | sed "s/ //g" | \
join -j 9999 - ${whitelistdir}/bc_gexscope_v2.txt | sed "s/ //g" | \
sort | uniq \
> ${whitelistdir}/GEXSCOPE-v2_barcodes.txt
fi
elif [[ "$technology" == "gexscope-v3.0.0" ]] || [[ "$technology" == "gexscope-v3.0.1" ]]; then
if [[ ! -f ${whitelistdir}/GEXSCOPE-v3_barcodes.txt ]]; then
#generates all combinations of R2 barcodes
join -j 9999 ${whitelistdir}/bc_gexscope_v3.txt ${whitelistdir}/bc_gexscope_v3..txt | sed "s/ //g" | \
join -j 9999 - ${whitelistdir}/bc_gexscope_v3.txt | sed "s/ //g" | \
sort | uniq \
> ${whitelistdir}/GEXSCOPE-v3_barcodes.tx
fi
elif [[ "$technology" == "icell8-full-length" ]]; then
if [[ ! -f ${whitelistdir}/SmartSeq_ICELL8_dual_barcodes.txt ]]; then
#generates all combinations of I1-I2 barcodes
Expand Down Expand Up @@ -3306,7 +3332,136 @@ else
echo " ${convFile} adjusted"
done
fi



#GEXSCOPE: remove linkers or Poly-T
##https://github.com/Hoohm/dropSeqPipe/issues/42
if [[ "$technology" == "gexscope-v1.0.0" ]]; then
echo " ... remove adapter for ${technology}"
for convFile in "${convFiles[@]}"; do
#remove poly-T
sed -E '
/.*(.{12})(.{8})T{18}/ {
s/.*(.{12})(.{8}).{18}/\1\2/g
n
n
s/.*(.{12})(.{8}).{18}/\1\2/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
done
fi
if [[ "$technology" == "gexscope-v2.0.0" ]] || [[ "$technology" == "gexscope-v2.1.0" ]]; then
echo " ... remove adapter for ${technology}"
for convFile in "${convFiles[@]}"; do
#remove phase blocks and linkers
sed -E '
/.*(.{8})ATCCACGTGCTTGAGA(.{8})TCAGCATGCGGCTACG(.{8})(.{12})T{18}/ {
s/.*(.{8})ATCCACGTGCTTGAGA(.{8})TCAGCATGCGGCTACG(.{8})(.{12})T{18}/\1\2\3\4/g
n
n
s/.*(.{8}).{16}(.{8}).{16}(.{8})(.{12}).{18}/\1\2\3\4/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
done
fi
if [[ "$technology" == "gexscope-v2.0.1" ]] || [[ "$technology" == "gexscope-v2.1.1" ]]; then
echo " ... remove adapter for ${technology}"
for convFile in "${convFiles[@]}"; do
#remove phase blocks and linkers
sed -E '
/.*(.{8})ATCCACGTGCTTGAGA(.{8})TCAGCATGCGGCTACG(.{8})C(.{12})T{18}/ {
s/.*(.{8})ATCCACGTGCTTGAGA(.{8})TCAGCATGCGGCTACG(.{8})C(.{12})T{18}/\1\2\3\4/g
n
n
s/.*(.{8}).{16}(.{8}).{16}(.{8}).{1}(.{12}).{18}/\1\2\3\4/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
done
fi
if [[ "$technology" == "gexscope-v3.0.0" ]]; then
echo " ... remove adapter for ${technology}"
for convFile in "${convFiles[@]}"; do
#remove phase blocks and linkers
sed -E '
/.*(.{9})ATCCACGTGCTTGAGA(.{9})TCAGCATGCGGCTACG(.{9})(.{12})T{18}/ {
s/.*(.{9})ATCCACGTGCTTGAGA(.{9})TCAGCATGCGGCTACG(.{9})(.{12})T{18}/\1\2\3\4/g
n
n
s/.*(.{9}).{16}(.{9}).{16}(.{9})(.{12}).{18}/\1\2\3\4/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
#remove 2nd linker
sed -E '
/.*(.{9})TCGGTGACAGCCATAT(.{9})CGTAGTCAGAAGCTGA(.{9})(.{12})T{18}/ {
s/.*(.{9})TCGGTGACAGCCATAT(.{9})CGTAGTCAGAAGCTGA(.{9})(.{12})T{18}/\1\2\3\4/g
n
n
s/.*(.{9}).{16}(.{9}).{16}(.{9})(.{12}).{18}/\1\2\3\4/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
#remove 3rd linker
sed -E '
/.*(.{9})CGAACATGTAGGTCTC(.{9})GACTACGTATTAGCAT(.{9})(.{12})T{18}/ {
s/.*(.{9})CGAACATGTAGGTCTC(.{9})GACTACGTATTAGCAT(.{9})(.{12})T{18}/\1\2\3\4/g
n
n
s/.*(.{9}).{16}(.{9}).{16}(.{9})(.{12}).{18}/\1\2\3\4/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
#remove 4th linker
sed -E '
/.*(.{9})GATTGTCACTAACGCG(.{9})ATGCTGACTCCTAGTC(.{9})(.{12})T{18}/ {
s/.*(.{9})GATTGTCACTAACGCG(.{9})ATGCTGACTCCTAGTC(.{9})(.{12})T{18}/\1\2\3\4/g
n
n
s/.*(.{9}).{16}(.{9}).{16}(.{9})(.{12}).{18}/\1\2\3\4/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
done
fi
if [[ "$technology" == "gexscope-v3.0.1" ]]; then
echo " ... remove adapter for ${technology}"
for convFile in "${convFiles[@]}"; do
#remove phase blocks and linkers
sed -E '
/.*(.{9})ATCCACGTGCTTGAGA(.{9})TCAGCATGCGGCTACG(.{9})C(.{12})T{18}/ {
s/.*(.{9})ATCCACGTGCTTGAGA(.{9})TCAGCATGCGGCTACG(.{9})C(.{12})T{18}/\1\2\3\4/g
n
n
s/.*(.{9}).{16}(.{9}).{16}(.{9}).{1}(.{12}).{18}/\1\2\3\4/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
#remove 2nd linker
sed -E '
/.*(.{9})TCGGTGACAGCCATAT(.{9})CGTAGTCAGAAGCTGA(.{9})C(.{12})T{18}/ {
s/.*(.{9})TCGGTGACAGCCATAT(.{9})CGTAGTCAGAAGCTGA(.{9})C(.{12})T{18}/\1\2\3\4/g
n
n
s/.*(.{9}).{16}(.{9}).{16}(.{9}).{1}(.{12}).{18}/\1\2\3\4/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
#remove 3rd linker
sed -E '
/.*(.{9})CGAACATGTAGGTCTC(.{9})GACTACGTATTAGCAT(.{9})C(.{12})T{18}/ {
s/.*(.{9})CGAACATGTAGGTCTC(.{9})GACTACGTATTAGCAT(.{9})C(.{12})T{18}/\1\2\3\4/g
n
n
s/.*(.{9}).{16}(.{9}).{16}(.{9}).{1}(.{12}).{18}/\1\2\3\4/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
#remove 4th linker
sed -E '
/.*(.{9})GATTGTCACTAACGCG(.{9})ATGCTGACTCCTAGTC(.{9})C(.{12})T{18}/ {
s/.*(.{9})GATTGTCACTAACGCG(.{9})ATGCTGACTCCTAGTC(.{9})C(.{12})T{18}/\1\2\3\4/g
n
n
s/.*(.{9}).{16}(.{9}).{16}(.{9}).{1}(.{12}).{18}/\1\2\3\4/g
}' $convFile > ${crIN}/.temp
mv ${crIN}/.temp $convFile
done
fi


#ICELL8 version 2 (non-UMI technology)
if [[ "$technology" == "icell8" ]] || [[ "$technology" == "icell8-5-prime" ]] || [[ "$technology" == "icell8-full-length" ]]; then
echo " ... filtering tagged reads for ${iechnology}"
Expand Down
0 whitelists/bc1_gexscope_v3.0.1 → whitelists/bc1_gexscope_v3.0.1.txt
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0 whitelists/bc2_gexscope_v3.0.1 → whitelists/bc2_gexscope_v3.0.1.txt
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0 whitelists/bc3_gexscope_v3.0.1 → whitelists/bc3_gexscope_v3.0.1.txt
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0 whitelists/bc_gexscope_v2 → whitelists/bc_gexscope_v2.txt
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0 whitelists/bc_gexscope_v3.0.1 → whitelists/bc_gexscope_v3.0.1.txt
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