Commit 7235a89c authored by Christoph's avatar Christoph
Browse files

deal with empty UMI tags

parent 5ccd394a

UMIstuffFUN.R

+1 −1
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@@ -251,7 +251,7 @@ ham_helper_fun <- function(x){ 
umiCollapseID<-function(reads,bccount,nmin=0,nmax=Inf,ftype=c("intron","exon"),...){

  retDF<-.sampleReads4collapsing(reads,bccount,nmin,nmax,ftype)

  if(!is.null(retDF)){

    nret<-retDF[, list(umicount = length(unique(UB[!is.na(UB)])),

    nret<-retDF[, list(umicount = length(unique(UB[!is.na(UB) & UB!=""])),

                       readcount =.N),

                by=c("RG","GE") ]

zUMIs-master.sh

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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=2.7.0a

vers=2.7.0b

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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