Merge pull request #175 from maxplanck-ie/fix_scRNAseq

Fix scRNAseq

snakePipes/workflows/scRNAseq/celseq_barcodes.192.txt

@@ -0,0 +1,192 @@
+1 AGTGTC
+2 ACCATG
+3 GAGTGA
+4 CACTCA
+5 CATGTC
+6 ACAGGA
+7 GTACCA
+8 ACAGAC
+9 ACGTTG
+10 ACCAAC
+11 GTGAAG
+12 CACTTC
+13 GAGTTG
+14 GAAGAC
+15 TGCAGA
+16 CTAGGA
+17 ACCAGA
+18 GTGACA
+19 CTAGAC
+20 AGCTCA
+21 ACTCGA
+22 CTGTTG
+23 CATGCA
+24 CAGAAG
+25 GTCTCA
+26 GTGATC
+27 TGTCTG
+28 GACAGA
+29 ACTCTG
+30 TGCAAC
+31 GAAGGA
+32 GTTGAG
+33 AGACCA
+34 TGGTTG
+35 GATCTG
+36 CTAGTG
+37 CTCAGA
+38 CTTCGA
+39 AGCTAG
+40 GATCGA
+41 GTACTC
+42 TGTCGA
+43 ACGTGA
+44 AGGATC
+45 CTCATG
+46 AGACTC
+47 GACAAC
+48 AGGACA
+49 ACTCAC
+50 GTACAG
+51 AGGAAG
+52 AGTGCA
+53 TGGTGA
+54 AGACAG
+55 AGCTTC
+56 TGAGGA
+57 ACGTAC
+58 TCACAG
+59 ACAGTG
+60 CGATTG
+61 TCTTGC
+62 GGTAAC
+63 TCATCC
+64 TAGGAC
+65 TTCACC
+66 AACGAG
+67 GTGGAA
+68 ATGTCG
+69 ATCACG
+70 GAATCC
+71 CGATGA
+72 GAATGG
+73 GCAACA
+74 TTCTCG
+75 ATTGCG
+76 TAGTGG
+77 AAGCCA
+78 CTATCC
+79 TCCGAA
+80 TGAACC
+81 TGTACG
+82 GACGAA
+83 CCACAA
+84 CACCAA
+85 CTAAGC
+86 GATACG
+87 ACAAGC
+88 TGAAGG
+89 TAACGG
+90 AACCTC
+91 CGTCTA
+92 CCATAG
+93 TTCCAG
+94 GGACAA
+95 ACTTCG
+96 TTGTGC
+97 GGTATG
+98 CTGCTA
+99 ATGAGG
+100 GGTAGA
+101 ATCGTG
+102 ATGGAC
+103 AGTAGG
+104 CCATCA
+105 AGTACC
+106 CCAGTA
+107 CGTTAC
+108 GAGGTA
+109 TTGGCA
+110 CAATGC
+111 GCGTTA
+112 TAGCTC
+113 TTCGAC
+114 GAGCAA
+115 TTGCTG
+116 TTGCGA
+117 GCAGAA
+118 CCTACA
+119 GCATGA
+120 AACTGG
+121 CGGTTA
+122 CTAACG
+123 CACGTA
+124 TTGGAG
+125 GCAATG
+126 TATCCG
+127 ATGCAG
+128 GCTCTA
+129 ATTCGC
+130 TGTTGG
+131 ATGACC
+132 CCGTAA
+133 TGATCG
+134 TACAGG
+135 AGAACG
+136 GCCATA
+137 ACGGTA
+138 AAGCAC
+139 CGAACA
+140 ATGCTC
+141 GGCTTA
+142 ATCGCA
+143 GGATCA
+144 CCAATC
+145 AAGGTG
+146 ATCTCC
+147 GTATCG
+148 TGTTCC
+149 GGTGTA
+150 TACTCC
+151 ATCAGC
+152 AAGTGC
+153 AGGCTA
+154 CCTATG
+155 TATCGC
+156 CGCTAA
+157 GTAACC
+158 ACATGG
+159 CCGATA
+160 GGATAC
+161 GTTAGG
+162 TACGCA
+163 AGATGC
+164 TTGCAC
+165 CAGGAA
+166 TCTAGG
+167 GCTTCA
+168 TTGGTC
+169 TACCGA
+170 CATTGG
+171 CTCGAA
+172 GCTTAC
+173 ATACGG
+174 GTATGC
+175 TGTAGC
+176 CGTAAG
+177 TTACGC
+178 TACCAC
+179 CGCATA
+180 GCTAAG
+181 ATCCAC
+182 CCTTGA
+183 AGCGAA
+184 GGTTAG
+185 GATTGC
+186 CGTTCA
+187 ATCCGA
+188 GCATTC
+189 CCTGAA
+190 GGAATC
+191 TCAACG
+192 AACACC

snakePipes/workflows/scRNAseq/scRNAseq_QC_metrics2.R

@@ -119,7 +119,7 @@ libs_per_plate = 2
 if (is_split_library) libs_per_plate = 4
 
 
-png(file=paste(out_prefix,".reads_UMI_plot.png",sep=""),width=1500,height=1500)
+pdf(file=paste(out_prefix,".reads_UMI_plot.pdf",sep=""))
 ggplot(dat=sc_dat,aes(x=(READS_UNIQFEAT),y=(UMI),color=sample))+geom_point(size=3,alpha=0.8) + 
  facet_wrap(~sample,ncol=libs_per_plate)+
  xlab("reads on feature per cell")+
@@ -148,7 +148,7 @@ if (num_samples>4){
 
 print(height)
 
-png(file=paste(out_prefix,".plate_cUPM.png",sep=""),width=1000,height=height)
+pdf(file=paste(out_prefix,".plate_cUPM.pdf",sep=""))
 
 ggplot(sc_dat,aes(x=x,y=y,fill=cUPM_zscore))+ 
  geom_tile() + 
@@ -165,7 +165,7 @@ ggplot(sc_dat,aes(x=x,y=y,fill=cUPM_zscore))+
 
 dev.off()
 
-png(file=paste(out_prefix,".plate_cRPM.png",sep=""),width=1000,height=height)
+pdf(file=paste(out_prefix,".plate_cRPM.png",sep="")) #,width=1000,height=height)
 
 ggplot(sc_dat,aes(x=x,y=y,fill=cRPM_zscore))+ 
  geom_tile() + 
@@ -182,7 +182,7 @@ ggplot(sc_dat,aes(x=x,y=y,fill=cRPM_zscore))+
 dev.off()
 
 
-png(file=paste(out_prefix,".plate_abs_transcripts.png",sep=""),width=1000,height=height)
+pdf(file=paste(out_prefix,".plate_abs_transcripts.png",sep="")) #,width=1000,height=height)
 
 ggplot(sc_dat,aes(x=x,y=y,fill=UMI))+ 
  geom_tile() +