Loading UMIstuffFUN.R +2 −1 Original line number Diff line number Diff line Loading @@ -260,7 +260,8 @@ umiCollapseID<-function(reads,bccount,nmin=0,nmax=Inf,ftype=c("intron","exon"),. if(n_nonUMI > 0 & n_nonUMI<nreads){ #detect mix of internal and UMI reads in Smartseq3 internaldt <- retDF[UB=="", list(readcount_internal =.N), by=c("RG","GE") ] nret <- merge(nret, internaldt, by = c("RG","GE")) nret <- merge(nret, internaldt, by = c("RG","GE"), all.x = TRUE) nret[is.na(readcount_internal), readcount_internal := 0] } return(nret) Loading zUMIs-master.sh +1 −1 Original line number Diff line number Diff line Loading @@ -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=2.7.1c vers=2.7.1d 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 Loading Loading
UMIstuffFUN.R +2 −1 Original line number Diff line number Diff line Loading @@ -260,7 +260,8 @@ umiCollapseID<-function(reads,bccount,nmin=0,nmax=Inf,ftype=c("intron","exon"),. if(n_nonUMI > 0 & n_nonUMI<nreads){ #detect mix of internal and UMI reads in Smartseq3 internaldt <- retDF[UB=="", list(readcount_internal =.N), by=c("RG","GE") ] nret <- merge(nret, internaldt, by = c("RG","GE")) nret <- merge(nret, internaldt, by = c("RG","GE"), all.x = TRUE) nret[is.na(readcount_internal), readcount_internal := 0] } return(nret) Loading
zUMIs-master.sh +1 −1 Original line number Diff line number Diff line Loading @@ -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=2.7.1c vers=2.7.1d 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 Loading
