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set up bacode whitelists for PIP-Seq versions 0-4
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@TomKellyGenetics
TomKellyGenetics committed Feb 6, 2024
1 parent b694c2b commit 7f05119
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58 changes: 55 additions & 3 deletions launch_universc.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -1735,7 +1735,7 @@ fi


#generate missing indexes if required (generating I1 and I2)
if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "icell8-full-length" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "smartseq2" ]] ||[[ "$technology" == "smartseq3" ]] || [[ "$technology" == "strt-seq-2i" ]] || [[ "$technology" == "strt-seq-2018" ]] || [[ "$technology" == "bravo" ]]; then
if [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "icell8-full-length" ]] || [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sciseq3" ]] || [[ "$technology" == "scifiseq" ]] || [[ "$technology" == "smartseq2" ]] ||[[ "$technology" == "smartseq3" ]] || [[ "$technology" == "strt-seq-2i" ]] || [[ "$technology" == "strt-seq-2018" ]] || [[ "$technology" == "bravo" ]] || [[ "$technology" == "vasa-drop" ]]; then
echo "dual indexes I1 and I2 required for $technology"
if [[ ${#index2[@]} -le 0 ]]; then
echo " automatically generating I1 and I2 index files from file headers"
Expand Down Expand Up @@ -1945,7 +1945,7 @@ if [[ -n "$barcodefile" ]]; then
barcodefile=$(readlink -f $barcodefile)
custombarcodes=true
#allowing WellList from ICELL8 and other well-based techniques
if [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "bd-rhapsody-v2" ]] || [[ "$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
if [[ "$technology" == "bd-rhapsody" ]] || [[ "$technology" == "bd-rhapsody-v2" ]] || [[ "$technology" == "bravo" ]] || [[ "$technology" == "celseq" ]] || [[ "$technology" == "celseq2" ]] || [[ "$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" ]] || [[ "$technology" == "pip-seq-v0" ]] || [[ "$technology" == "pip-seq-v1" ]] || [[ "$technology" == "pip-seq-v2" ]] || [[ "$technology" == "pip-seq-v3" ]] || [[ "$technology" == "pip-seq-v4" ]] || [[ "$technology" == "vasa-plate" ]] || [[ "$technology" == "custom" ]]; then
seg=$'\t'
n_col=$(awk -F'\t' '{print NF}' $barcodefile | sort -nu | tail -n 1)
if [[ $n_col -eq 1 ]]; then
Expand Down Expand Up @@ -1994,7 +1994,7 @@ else
if [[ ! -f ${whitelistdir}/bc_celseq1.txt ]]; then
echo " generating combination of I1, I2, and RT barcodes ..."
fi
elif [[ "$technology" == "celseq2" ]] || [[ "$technology" == "vasa-plate" ]]; then
elif [[ "$technology" == "celseq2" ]]; then
barcodefile=${whitelistdir}/bc_celseq2.txt
if [[ ! -f ${whitelistdir}/bc_celseq2.txt ]]; then
echo " generating combination of I1, I2, and RT barcodes ..."
Expand Down Expand Up @@ -2057,6 +2057,26 @@ else
barcodefile=${whitelistdir}/inDrop-v3_barcodes.txt
echo "***WARNING: combination of list1 and list2 from indrop-v2 (https://github.com/indrops/indrops/issues/32)***"
fi
elif [[ "$technology" == "pip-seq-v0" ]]; then
barcodefile=${whitelistdir}/pip-seq-v0_barcodes.txt
if [[ ! -f ${whitelistdir}/pip-seq-v0_barcodes.txt ]]; then
echo " generating combination of barcodes ..."
fi
elif [[ "$technology" == "pip-seq-v1" ]]; then
barcodefile=${whitelistdir}/pip-seq-v1_barcodes.txt
if [[ ! -f ${whitelistdir}/pip-seq-v1_barcodes.txt ]]; then
echo " generating combination of barcodes ..."
fi
elif [[ "$technology" == "pip-seq-v2" ]]; then
barcodefile=${whitelistdir}/pip-seq-v2_barcodes.txt
if [[ ! -f ${whitelistdir}/pip-seq-v2_barcodes.txt ]]; then
echo " generating combination of barcodes ..."
fi
elif [[ "$technology" == "pip-seq-v3" ]] || [[ "$technology" == "pip-seq-v4" ]]; then
barcodefile=${whitelistdir}/pip-seq-v3_barcodes.txt
if [[ ! -f ${whitelistdir}/pip-seq-v3_barcodes.txt ]]; then
echo " generating combination of barcodes ..."
fi
elif [[ "$technology" == "sciseq2" ]]; then
barcodefile=${whitelistdir}/sciseq2_barcode.txt
if [[ ! -f ${whitelistdir}/sciseq2_barcode.txt ]]; then
Expand Down Expand Up @@ -2192,6 +2212,38 @@ else
sort | uniq \
> ${whitelistdir}/microwellseq_barcode.txt
fi
elif [[ "$technology" == "pip-seq-v0" ]]; then
if [[ ! -f ${whitelistdir}/pip-seq-v0_barcodes.txt ]]; then
#generates all combinations of R1 barcodes
join -j 9999 ${whitelistdir}/pip-seq_v0_bc1.tsv ${whitelistdir}/pip-seq_v0_bc2.tsv | sed "s/ //g" | \
join -j 9999 - ${whitelistdir}/pip-seq_v0_bc3.tsv | sed "s/ //g" | \
sort | uniq \
> ${whitelistdir}/pip-seq-v0_barcodes.txt
fi
elif [[ "$technology" == "pip-seq-v1" ]]; then
if [[ ! -f ${whitelistdir}/pip-seq-v1_barcodes.txt ]]; then
#generates all combinations of R1 barcodes
join -j 9999 ${whitelistdir}/pip-seq_v1_bc1.tsv ${whitelistdir}/pip-seq_v1_bc1.tsv | sed "s/ //g" | \
sort | uniq \
> ${whitelistdir}/pip-seq-v1_barcodes.txt
fi
elif [[ "$technology" == "pip-seq-v2" ]]; then
if [[ ! -f ${whitelistdir}/pip-seq-v2_barcodes.txt ]]; then
#generates all combinations of R1 barcodes
join -j 9999 ${whitelistdir}/pip-seq_v2_bc1.tsv ${whitelistdir}/pip-seq_v2_bc2.tsv | sed "s/ //g" | \
join -j 9999 - ${whitelistdir}/pip-seq_v2_bc3.tsv | sed "s/ //g" | \
sort | uniq \
> ${whitelistdir}/pip-seq-v2_barcodes.txt
fi
elif [[ "$technology" == "pip-seq-v3" ]] | [[ "$technology" == "pip-seq-v4" ]]; then
if [[ ! -f ${whitelistdir}/pip-seq-v4_barcodes.txt ]]; then
#generates all combinations of R1 barcodes
join -j 9999 ${whitelistdir}/pip-seq_v3_bc1.tsv ${whitelistdir}/pip-seq_v2_bc3.tsv | sed "s/ //g" | \
join -j 9999 - ${whitelistdir}/pip-seq_v3_bc3.tsv | sed "s/ //g" | \
join -j 9999 - ${whitelistdir}/pip-seq_v3_bc4.tsv | sed "s/ //g" |
sort | uniq \
> ${whitelistdir}/pip-seq-v3_barcodes.txt
fi
elif [[ "$technology" == "sciseq2" ]]; then
if [[ ! -f ${whitelistdir}/sciseq2_barcode.txt ]]; then
#generates all combinations of I1-I2-R2 barcodes
Expand Down
0 whitelists/pip-seq-v1_barcodes.txt → whitelists/pip-seq_v0_bc1.tsv
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File renamed without changes.
96 changes: 96 additions & 0 deletions whitelists/pip-seq_v0_bc2.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,96 @@
CTATGGAG
CAGTAAGG
AGAGTTCG
GACCATAC
AGGTCCTA
AATGCAGC
TGTGTGCT
ACCTAGCA
TCCTTCAC
GGTCTACA
CAGTCGAA
ATGCCACA
ATACGTGC
GATGACTC
GTGTAACC
AGGAACGT
GACTTGAG
CGACTCTT
ACGTCAAC
ACGCTTGT
ACTTCGGT
TCGCATTC
ACACTCAG
GTTCCAAG
CGTGCATA
TGAGGATG
CTCGTGAT
AACAACCG
CTCACAGT
CGCCTTAA
AGTGGTAC
AATCGCCT
CCTGGAAT
CTTCTCGA
AACACGAC
CCAACGAT
GGATTGTC
GCGTTATG
CAAGACCT
ACCTGTTG
AACCAGGT
AGCTTACC
TTAACGCG
ACAATGCC
CGACAAGA
ATATCCGG
GATCGGTA
ACAAGAGG
TCGAACCA
TACGGTCT
TGTCAGTG
TCATGCGT
CAACCTAG
GTACACCA
CACTTCCA
AAGAGGCA
ACCGCTAA
GTCAGAAC
ACACCGTA
CCAGTTAC
TTGTTCCG
AACGGAAG
ACAGCACT
AACCTCTC
TTCCGCTT
ATGTTGGC
CTGGTTCA
AGCATGGA
GGCTCAAT
CTAAGCTC
ACTGACGA
CCATACTG
GCTATTCG
CGGAATTG
AAGACTGG
AGGTAGAG
GGCAATCT
ACCGAATC
AAGGATCC
CCGATGTA
CTTCCTTC
CGTAGGTT
CAGAACAC
GCAAGCAA
GAGAGAGT
TTCTGAGG
CAAGGTGA
GAATCACG
AGCACATG
GAACTGCT
GGACGTAT
CCTCATCT
CTTAGTGG
TCCGTAGT
GTGGTCTT
ATTGGCTG
96 changes: 96 additions & 0 deletions whitelists/pip-seq_v0_bc3.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,96 @@
ACGCTTGT
AGCTTACC
GTTCCAAG
AGCACATG
ACACCGTA
TCATGCGT
CCAACGAT
AACACGAC
CCTCATCT
CCAGTTAC
GTGGTCTT
GTCAGAAC
CAGAACAC
ACCTGTTG
ATGTTGGC
CTTAGTGG
GCAAGCAA
AGTGGTAC
CTTCTCGA
CTATGGAG
ACGTCAAC
TCCGTAGT
TTGTTCCG
GGATTGTC
CAGTAAGG
CCATACTG
CGGAATTG
AACCAGGT
TGTGTGCT
CTAAGCTC
AGCATGGA
CAAGGTGA
CAACCTAG
CTTCCTTC
TCCTTCAC
AAGAGGCA
TGAGGATG
TACGGTCT
GATCGGTA
AACAACCG
CGTGCATA
AACCTCTC
AATGCAGC
ACCTAGCA
ATGCCACA
CTCGTGAT
ATACGTGC
ACACTCAG
AGGAACGT
AATCGCCT
AACGGAAG
ACAATGCC
GAATCACG
ACCGCTAA
TGTCAGTG
GACCATAC
AGGTAGAG
ACAGCACT
TTAACGCG
ATATCCGG
CGACAAGA
AGAGTTCG
CACTTCCA
GACTTGAG
GGCTCAAT
CTGGTTCA
GGCAATCT
CGACTCTT
CAAGACCT
ACTGACGA
CCTGGAAT
CCGATGTA
TTCTGAGG
TCGAACCA
CGCCTTAA
CGTAGGTT
AAGGATCC
GCGTTATG
GTACACCA
ACCGAATC
GGTCTACA
GTGTAACC
AAGACTGG
TCGCATTC
CAGTCGAA
GAGAGAGT
AGGTCCTA
ACTTCGGT
GATGACTC
ATTGGCTG
GGACGTAT
GCTATTCG
GAACTGCT
ACAAGAGG
CTCACAGT
TTCCGCTT
96 changes: 96 additions & 0 deletions whitelists/pip-seq_v1_bc1.tsv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,96 @@
TCCGTAGT
TCCTTCAC
AACACGAC
ACAGCACT
CTCACAGT
GGTCTACA
AAGACTGG
CACTTCCA
ATGCCACA
GGACGTAT
CTTCCTTC
GGCAATCT
AACCTCTC
CAAGGTGA
CCATACTG
CGTGCATA
TCGCATTC
ACAATGCC
AACAACCG
CCGATGTA
GAGAGAGT
GATCGGTA
GACTTGAG
AGGTCCTA
GATGACTC
CCAACGAT
TGAGGATG
CAACCTAG
AAGAGGCA
AGCTTACC
AATCGCCT
ACCGAATC
ATATCCGG
AATGCAGC
CTAAGCTC
ACACTCAG
CAGTCGAA
CCAGTTAC
CGGAATTG
CCTGGAAT
TTCTGAGG
CGTAGGTT
TTCCGCTT
ACTGACGA
ACAAGAGG
GCAAGCAA
AGGTAGAG
CAAGACCT
TACGGTCT
TTAACGCG
CTTAGTGG
ACCTGTTG
GGCTCAAT
ATTGGCTG
ACCGCTAA
CCTCATCT
AACCAGGT
GAATCACG
GTTCCAAG
GGATTGTC
GTGTAACC
AGCATGGA
CGACTCTT
AGTGGTAC
ACTTCGGT
CGACAAGA
GCGTTATG
TCGAACCA
ACGTCAAC
GTACACCA
GTGGTCTT
GCTATTCG
TCATGCGT
CGCCTTAA
CAGTAAGG
ACACCGTA
TTGTTCCG
AGAGTTCG
CAGAACAC
CTCGTGAT
TGTGTGCT
AAGGATCC
ATGTTGGC
CTATGGAG
AACGGAAG
CTTCTCGA
AGGAACGT
ACCTAGCA
GAACTGCT
ATACGTGC
GACCATAC
ACGCTTGT
GTCAGAAC
AGCACATG
CTGGTTCA
TGTCAGTG
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