configure inputs for PIP-Seq and VASA-Seq

launch_universc.sh

@@ -800,14 +800,14 @@ elif [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "smart-seq3" ]];
     nonUMI=false
 elif [[ "$technology" == "splitseq" ]] || [[ "$technology" == "split-seq" ]]; then
     technology="splitseq"
-elif [[ "$technology" == "splitseq2" ]] || [[ "$technology" == "split-seq2" ]] || [[ "$technology" == "splitseq-v2" ]] || [[ "$technology" == "split-seq-v2" ]] || [[ "$technology" == "parse" ]] || [[ "$technology" == "parsebio" ]]|| [[ "$technology" == "parse-bio" ]] || [[ "$technology" == "evercode" ]]; then
+elif [[ "$technology" == "splitseq2" ]] || [[ "$technology" == "split-seq2" ]] || [[ "$technology" == "splitseq-v2" ]] || [[ "$technology" == "split-seq-v2" ]] || [[ "$technology" == "parse" ]] || [[ "$technology" == "parsebio" ]] || [[ "$technology" == "parse-bio" ]] || [[ "$technology" == "evercode" ]]; then
     technology="splitseq2"
 elif [[ "$technology" == "strt-seq" ]] || [[ "$technology" == "strt" ]] || [[ "$technology" == "strtseq" ]]; then
     technology="strt-seq"
     nonUMI=true
     if [[ -z ${chemistry} ]] || [[ ${chemistry} == "SC3Pv"* ]]; then
         if [[ $verbose ]]; then
-            echo "setting chemistry for 5' scRNA"
+            echo "setting chemistry for 5\' scRNA"
         fi
         chemistry="SC5P-R1"
     fi
@@ -819,7 +819,7 @@ elif [[ "$technology" == "strt-seq-2018" ]] || [[ "$technology" == "strt-seqc201
     technology="strt-seq-2018"
     if [[ -z ${chemistry} ]] || [[ ${chemistry} == "SC5P"* ]]; then
         if [[ $verbose ]]; then
-            echo "setting chemistry for 3' scRNA PE"
+            echo "setting chemistry for 3\' scRNA PE"
         fi
         chemistry="SC3Pv2"
      fi
@@ -1027,7 +1027,7 @@ elif [[ "$technology" == "strt-seq-2i" ]]; then
     barcodelength=13
     umilength=6
     minlength=13
-if [[ "$technology" == "strt-seq-2018" ]]; then
+elif [[ "$technology" == "strt-seq-2018" ]]; then
     barcodelength=8
     umilength=8
     minlength=8
@@ -1048,7 +1048,6 @@ elif [[ "$technology" == "custom"* ]]; then
     umilength=`echo $technology | cut -f 3 -d'_'`
     minlength=${barcodelength}
 fi
-
 if [[ $verbose ]]; then
     echo " barcode and UMI lengths set as ${barcodelength} and ${umilength} respectively"
 fi
@@ -2010,7 +2009,7 @@ else
         if [[ -f $(echo ${index2}([0])) ]]; then
             index2length=$(($(head $index2([0]) -n 2 | tail -n 1 | wc -c) -1))
             barcodelength=$(($indexlength+$index2length))
-            if [[ -f ${whitelistdir}/Illumina_dual_barcodes.txt ]];then
+            if [[ -f ${whitelistdir}/Illumina_dual_barcodes.txt ]]; then
                 cat ${whitelistdir}/Illumina_TruSeq_Index1_i7_barcodes.txt ${whitelistdir}/Illumina_Nextera_Index1_i7_barcodes.txt | sort | uniq > ${whitelistdir}/Illumina_Index1_i7_barcodes.txt
                 cat ${whitelistdir}/Illumina_TruSeq_Index2_i5_barcodes.txt ${whitelistdir}/Illumina_Nextera_Index2_i5_barcodes.txt | sort | uniq > ${whitelistdir}/Illumina_Index2_i5_barcodes.txt
                 join -j 9999 ${whitelistdir}/Illumina_Index1_i7_barcodes.txt ${whitelistdir}/Illumina_Index2_i5_barcodes.txt | sed "s/ //g" > ${whitelistdir}/Illumina_dual_barcodes.txt
@@ -2071,7 +2070,7 @@ else
          barcodefile=${whitelistdir}/STRTSeqC1_barcode.txt
     elif [[ "$technology" == "strt-seq-2i" ]]; then
          barcodefile=${whitelistdir}/STRTSeq2i_barcode.txt
-    elif  [[ "$technology" == "strt-seq-2018" ]];
+    elif  [[ "$technology" == "strt-seq-2018" ]]; then
          barcodefile=${whitelistdir}/strt_fan2018_barcode_96_8bp.txt
     else
         echo "***WARNING: whitelist for ${technology} will be all possible combinations of ${minlength} bp. valid barcode will be 100% as a result***"

whitelists/fb_v3_bc1.tsv

@@ -0,0 +1,96 @@
+AGAAACCA
+GATTTCCC
+AAGTCCAA
+GAGAAACC
+GCCTGGTA
+AATATGAC
+GAAATACG
+TATCTGTC
+AGACGAGG
+TCCGACAC
+ACCAGTTT
+GAATCCCA
+GTGAGGCA
+ACCAACCC
+AAACAAAC
+ACCCATGC
+ATTACCTT
+AAACTACA
+CTCCTCCA
+CACTAACC
+AATACATC
+AGTCACAA
+TAACTTCT
+ATACTCTC
+CAATTCTC
+TCTATTCC
+TACCTCCC
+TCCTATAT
+AAATTCCG
+CAAACATT
+CCATCCAC
+GTCTAATC
+CCACCTCT
+TACCCTGC
+GTGTCACC
+ACTACCCG
+AGTTGAAC
+CAGGTTGC
+AAACCGCC
+GTCCACTA
+CCTCATGA
+TACTGAAT
+AAGTTGTC
+CTGTTGTG
+GAGTGTAC
+AGGACACA
+TTCACTGG
+GAGGGTCA
+CCCTGTTT
+GAGGAGTG
+GTGAACTC
+ATCCCACC
+AGACCTCA
+CCTACGCT
+ACCTTCCC
+AAGGGACC
+GTAAACAA
+ACCCTCAA
+CCTATTTA
+TTGACCCA
+GTCTTCCT
+CTAGACTA
+TAGTCTCT
+AGAGGTGC
+CCTTTACA
+CTGTGACC
+GATTACTT
+GTGGTGCT
+CCCTCTTG
+AAAGAGGC
+CTGGGTAT
+CTAACGCC
+TATGTGAA
+TCTAAACT
+CTGTTTCC
+CCTTTGTC
+ATACACCC
+TTCCCTAT
+GACACCTG
+CCCTTGCA
+GTTGTCCG
+TTGGGTCC
+TATCCACG
+CTTTCACT
+CAAGGGTT
+ATTTCCAT
+CTTTGGAC
+AGTTTGTA
+CTTAGTGT
+GATGTGGC
+TCCCTGGA
+CTTTATCC
+GATTGGGA
+CTTCTACG
+GTCCTTGC
+TCTTTGAC

whitelists/fb_v3_bc2.tsv

@@ -0,0 +1,96 @@
+TCTGTG
+GAGATA
+GATGAA
+GAAATC
+AGGTAA
+CAATAC
+AAAGTG
+TATGCC
+GTTAGT
+AGAAGG
+TCTACC
+TGCTAG
+AAAGGC
+CTATGG
+ATCTGA
+ATGCAC
+GATTTC
+ACAAAG
+CATCTA
+GCTGTA
+CTTGTT
+ACAGCA
+GTGATC
+TAAGGC
+ACATGT
+ACAACC
+AGTGGA
+AAACAC
+TAGCGA
+GCTAAG
+AGACGT
+ATCAAC
+CTGGTA
+GTTTGG
+ATGTTG
+ACTTCC
+AATAGC
+AAGAGA
+GAACAG
+GCTCTT
+CCGTAT
+TACAGA
+GCACTA
+AATACC
+TTGGTA
+TGCTTT
+CACATT
+TGGGTT
+TAAGCC
+AAGGTG
+TGAGAA
+AGTTAC
+TTGGCA
+CACGAA
+CACAAG
+TAGTCT
+CCAAAT
+AAGCAC
+GTACAA
+CGCAAA
+TGAACC
+CCTAAT
+TATTGG
+GACAAT
+CTGAAG
+GAAGAA
+GCGTTT
+TCAGTC
+GTTGCT
+TTCGAA
+GGTTTC
+GGTCTA
+CTTGAC
+TAACCC
+CAGTTG
+AGGAAA
+AAAGAC
+CTTCGA
+GATATG
+AAACCG
+CTTTAG
+GAAAGG
+TTTCTC
+GTAGAG
+GTTCAC
+AACTGA
+AGAAAC
+TGAAAG
+TGTATC
+TCAAAG
+ACGGTT
+CTAAAG
+TTAACG
+ACCTTT
+TCGATT
+GTAATC

whitelists/fb_v3_bc3.tsv

@@ -0,0 +1,96 @@
+AAAGTG
+AACTGA
+TAGCGA
+GTAGAG
+GTTAGT
+GTAATC
+ATCTTC
+AGGTAA
+GTGATC
+GTTGCT
+CACGAA
+CACATT
+GCACTA
+GAAATC
+GACAAT
+AAGCTC
+AGGAAA
+TGTATC
+AAACTC
+GAAAGG
+ACAACC
+CTGGTA
+ACAAAG
+AAGCAC
+AAAGGC
+TGAAAG
+TGTAAC
+TGAGAA
+GTTTGG
+GTACAA
+ACAGCA
+TCAAAG
+TACTCA
+CAAACA
+CACAAG
+TGGGTT
+TGAACC
+CCAAAT
+TAAGGC
+ACCTTT
+TTGGTA
+GATATG
+GCTGTA
+ACCATA
+AGAAGG
+CTTGTT
+TAGAAC
+CTAAAG
+ACTTCC
+GATACC
+AAAGAC
+TATTGG
+GAAACC
+TGCTTT
+AGTGGA
+ATGTTG
+ATCAAC
+CTTGAC
+ATGCAC
+AGACGT
+CTATGG
+TACAGA
+GCTAAG
+CAATAC
+AATACC
+AAACCG
+TTAACG
+CTTCGA
+TCCATA
+GGTTTC
+ATCTGA
+CAGTTG
+TCTACC
+TAACCC
+AAACAC
+GCGTTT
+TATGCC
+CTTTAG
+AAGGTG
+AGAAAC
+AAGAGA
+CCTAAT
+TAAGCC
+TTCCAG
+GAAGAA
+GAACAG
+TCAGTC
+TCTGTG
+TTGGCA
+GTTCAC
+AATAGC
+TGCTAG
+ACATGT
+CTTCCA
+AGTTAC
+CTGAAG