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zUMIs2.5 improve BC error correction
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| #!/usr/bin/perl | ||
| use warnings; | ||
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| if(@ARGV != 4) | ||
| { | ||
| "\n##################################################################################### | ||
| Usage: perl $0 <inbam> <outbam> <BCbinmap> <samtools-executable> \n | ||
| Please drop your suggestions and clarifications to <christoph.ziegenhain\@ki.se>\n | ||
| ######################################################################################\n\n"; | ||
| exit; | ||
| } | ||
| BEGIN{ | ||
| $inbam=$ARGV[0]; | ||
| $outbam=$ARGV[1]; | ||
| $binmap=$ARGV[2]; | ||
| $samtoolsexc=$ARGV[3]; | ||
| } | ||
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| open(INBAM, "$samtoolsexc view $inbam | sed 's/BC:Z://' | " ) || die "Couldn't open file $inbam. Check permissions!\n Check if it is a bam file and it exists\n\n"; | ||
| open(BCBAM,"| $samtoolsexc view -b -o $outbam -"); | ||
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| my %bcmap; | ||
| open(DATA, "cat $binmap | sed 's/,/\t/g' | cut -f1,3 | grep -v 'falseBC' | ") || die "Can't open $binmap ! \n"; | ||
| while (<DATA>) { | ||
| my ($raw, @fixedBC) = split(/\t/); | ||
| $bcmap{$raw} = \@fixedBC; | ||
| } | ||
| close DATA; | ||
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| while (<INBAM>) { | ||
| $read=$_; | ||
| chomp($read); | ||
| @read = split(/\t/,$read); | ||
| $thisBC = $read[11]; | ||
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| if (defined($bcmap{$thisBC})) { | ||
| #print "BC is in hash\n"; | ||
| $correctBC = $bcmap{$thisBC}[0]; | ||
| chomp($correctBC); | ||
| } | ||
| else { | ||
| #print "BC is not in hash\n"; | ||
| $correctBC = $thisBC; | ||
| } | ||
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| print BCBAM $read[0],"\t",$read[1],"\t",$read[2],"\t",$read[3],"\t",$read[4],"\t",$read[5],"\t",$read[6],"\t",$read[7],"\t",$read[8],"\t", | ||
| $read[9],"\t",$read[10],"\t","BX:Z:",$thisBC,"\t","BC:Z:",$correctBC,"\t",$read[12],"\n"; | ||
|
|
||
| } | ||
| close INBAM; | ||
| close BCBAM; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| #!/usr/bin/env Rscript | ||
| library(methods) | ||
| library(data.table) | ||
| library(yaml) | ||
| library(ggplot2) | ||
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| ########################## | ||
| myYaml <- commandArgs(trailingOnly = T) | ||
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| opt <-read_yaml(myYaml) | ||
| setwd(opt$out_dir) | ||
| source(paste0(opt$zUMIs_directory,"/barcodeIDFUN.R")) | ||
| options(datatable.fread.input.cmd.message=FALSE) | ||
| data.table::setDTthreads(threads=opt$num_threads) | ||
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| ####################################################################### | ||
| ####################################################################### | ||
| ##### Barcode handling & chunking | ||
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| #read file with barcodecounts | ||
| # bc is the vector of barcodes to keep | ||
| bccount<-cellBC(bcfile = opt$barcodes$barcode_file, | ||
| bcnum = opt$barcodes$barcode_num, | ||
| bcauto = opt$barcodes$automatic, | ||
| bccount_file= paste0(opt$out_dir,"/", opt$project, ".BCstats.txt"), | ||
| outfilename = paste0(opt$out_dir,"/zUMIs_output/stats/",opt$project,".detected_cells.pdf")) | ||
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| fwrite(bccount,file=paste0(opt$out_dir,"/zUMIs_output/",opt$project,"kept_barcodes.txt")) | ||
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| #check if binning of adjacent barcodes should be run | ||
| if(opt$barcodes$BarcodeBinning > 0){ | ||
| binmap <- BCbin(bccount_file = paste0(opt$out_dir,"/", opt$project, ".BCstats.txt"), | ||
| bc_detected = bccount) | ||
| fwrite(binmap,file=paste0(opt$out_dir,"/zUMIs_output/",opt$project,".BCbinning.txt")) | ||
| #update the number reads in BCcount table | ||
| binmap_additional <- binmap[, .(addtl = sum(n)), by = trueBC] | ||
| bccount[match(binmap_additional$trueBC,XC),n := n + binmap_additional$addtl] | ||
| fwrite(bccount,file=paste0(opt$out_dir,"/zUMIs_output/",opt$project,"kept_barcodes_binned.txt")) | ||
| } | ||
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| ############################################################## | ||
| q() |
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