Commit 5ccd394a authored by Christoph's avatar Christoph
Browse files

fix merging bug with too many cells

parent 22ecf3a4

UMIstuffFUN.R

+4 −2
Original line number Diff line number Diff line
@@ -369,9 +369,11 @@ correct_UB_tags <- function(bccount, samtoolsexc){ 
  bla <- parallel::mclapply(UB_cmd_list, system ,mc.cores = opt$num_threads, mc.preschedule=F)

  UB_cmd_list <- unlist(UB_cmd_list)

  UB_files <- as.character(data.frame(strsplit(UB_cmd_list," "),stringsAsFactors=F)[3,])

  UB_files <- paste(UB_files, collapse = " ")

  #UB_files <- paste(UB_files, collapse = " ")

  UB_mergelist <- paste0(opt$out_dir,"/zUMIs_output/molecule_mapping/",opt$project,"mergelist.txt")

  write(UB_files, file = UB_mergelist)

  outbam <- paste0(opt$out_dir,"/",opt$project,".filtered.Aligned.GeneTagged.UBcorrected.bam")

  merge_cmd <- paste(samtoolsexc,"merge -n -t BC -@",opt$num_threads,outbam,UB_files)

  merge_cmd <- paste(samtoolsexc,"merge -n -t BC -@",opt$num_threads,"-b",UB_mergelist,outbam)

  write(merge_cmd, file = paste0(opt$out_dir,"/",opt$project,".merge.sh"))

  system(paste0("bash ",opt$out_dir,"/",opt$project,".merge.sh"))

  return(outbam)

zUMIs-master.sh

+1 −1
Original line number Diff line number Diff line
@@ -3,7 +3,7 @@ 
# Pipeline to run UMI-seq analysis from fastq to read count tables.

# Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann

# Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se

vers=2.7.0

vers=2.7.0a

currentv=`curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/master/zUMIs-master.sh | grep '^vers=' | cut -f2 -d "="`

if [ "$currentv" != "$vers" ]; then echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------"; fi

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