Loading zUMIs-mapping.sh +1 −0 Original line number Diff line number Diff line Loading @@ -13,6 +13,7 @@ starexc=$8 samtoolsexc=$9 xm="${10}" bt="${11}" isstrt="${12}" if [[ "$isstrt" == "no" ]] ; then rl=`expr $r - 1` Loading zUMIs-master.sh +2 −2 Original line number Diff line number Diff line Loading @@ -223,13 +223,13 @@ if [[ "$isslurm" == "yes" ]] ; then else bash $zumisdir/zUMIs-filtering-strt.sh $cdnaread $bcread $sname $outdir $xmrange $cbasequal $mbasequal $molbcbase $cellbcbase $threads $zumisdir $bcread2 $BaseTrim fi bash $zumisdir/zUMIs-mapping.sh $sname $outdir $genomedir $gtf $threads $readlen "$starparams" $starexc $samtoolsexc $xmrange $BaseTrim bash $zumisdir/zUMIs-mapping.sh $sname $outdir $genomedir $gtf $threads $readlen "$starparams" $starexc $samtoolsexc $xmrange $BaseTrim $isstrt bash $zumisdir/zUMIs-prepCounting.sh $sname $outdir $threads $samtoolsexc bash $zumisdir/zUMIs-counting.sh $sname $outdir $barcodes $threads $gtf $strandedness $xcrange $xmrange $subsampling $zumisdir $isStats $whichStage $isstrt $bcread2 $xcrange2 bash $zumisdir/zUMIs-cleaning.sh $sname $outdir ;; "mapping") bash $zumisdir/zUMIs-mapping.sh $sname $outdir $genomedir $gtf $threads $readlen "$starparams" $starexc $samtoolsexc $xmrange $BaseTrim bash $zumisdir/zUMIs-mapping.sh $sname $outdir $genomedir $gtf $threads $readlen "$starparams" $starexc $samtoolsexc $xmrange $BaseTrim $isstrt bash $zumisdir/zUMIs-prepCounting.sh $sname $outdir $threads $samtoolsexc bash $zumisdir/zUMIs-counting.sh $sname $outdir $barcodes $threads $gtf $strandedness $xcrange $xmrange $subsampling $zumisdir $isStats $whichStage $isstrt $bcread2 $xcrange2 bash $zumisdir/zUMIs-cleaning.sh $sname $outdir Loading Loading
zUMIs-mapping.sh +1 −0 Original line number Diff line number Diff line Loading @@ -13,6 +13,7 @@ starexc=$8 samtoolsexc=$9 xm="${10}" bt="${11}" isstrt="${12}" if [[ "$isstrt" == "no" ]] ; then rl=`expr $r - 1` Loading
zUMIs-master.sh +2 −2 Original line number Diff line number Diff line Loading @@ -223,13 +223,13 @@ if [[ "$isslurm" == "yes" ]] ; then else bash $zumisdir/zUMIs-filtering-strt.sh $cdnaread $bcread $sname $outdir $xmrange $cbasequal $mbasequal $molbcbase $cellbcbase $threads $zumisdir $bcread2 $BaseTrim fi bash $zumisdir/zUMIs-mapping.sh $sname $outdir $genomedir $gtf $threads $readlen "$starparams" $starexc $samtoolsexc $xmrange $BaseTrim bash $zumisdir/zUMIs-mapping.sh $sname $outdir $genomedir $gtf $threads $readlen "$starparams" $starexc $samtoolsexc $xmrange $BaseTrim $isstrt bash $zumisdir/zUMIs-prepCounting.sh $sname $outdir $threads $samtoolsexc bash $zumisdir/zUMIs-counting.sh $sname $outdir $barcodes $threads $gtf $strandedness $xcrange $xmrange $subsampling $zumisdir $isStats $whichStage $isstrt $bcread2 $xcrange2 bash $zumisdir/zUMIs-cleaning.sh $sname $outdir ;; "mapping") bash $zumisdir/zUMIs-mapping.sh $sname $outdir $genomedir $gtf $threads $readlen "$starparams" $starexc $samtoolsexc $xmrange $BaseTrim bash $zumisdir/zUMIs-mapping.sh $sname $outdir $genomedir $gtf $threads $readlen "$starparams" $starexc $samtoolsexc $xmrange $BaseTrim $isstrt bash $zumisdir/zUMIs-prepCounting.sh $sname $outdir $threads $samtoolsexc bash $zumisdir/zUMIs-counting.sh $sname $outdir $barcodes $threads $gtf $strandedness $xcrange $xmrange $subsampling $zumisdir $isStats $whichStage $isstrt $bcread2 $xcrange2 bash $zumisdir/zUMIs-cleaning.sh $sname $outdir Loading
