Loading zUMIs-master.sh +2 −2 Original line number Original line Diff line number Diff line Loading @@ -3,7 +3,7 @@ # Pipeline to run UMI-seq analysis from fastq to read count tables. # Pipeline to run UMI-seq analysis from fastq to read count tables. # Authors: Swati Parekh & Christoph Ziegenhain # Authors: Swati Parekh & Christoph Ziegenhain # Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se or hellmann@bio.lmu.de # Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se or hellmann@bio.lmu.de vers=0.0.6c vers=0.0.6d function check_opts() { function check_opts() { value=$1 value=$1 name=$2 name=$2 Loading Loading @@ -42,7 +42,7 @@ Make sure you have 3-4 times more disk space to your input fastq files. For STRT-seq give this as 1-n where n is your first cell barcode(-f) length. For STRT-seq give this as 1-n where n is your first cell barcode(-f) length. For InDrops give this as 1-n where n is the total length of cell barcode (8bp BC part1 + 6bp library barcode + 8bp BC part2) (e.g. 1-22). For InDrops give this as 1-n where n is the total length of cell barcode (8bp BC part1 + 6bp library barcode + 8bp BC part2) (e.g. 1-22). -m <XM baserange> : Base range for UMI barcode in -f Barcode read(e.g. 7-16). Required. -m <XM baserange> : Base range for UMI barcode in -f Barcode read(e.g. 7-16). Required. For STRT-seq/InDrops give this as 1-n where n is your UMI length. For STRT-seq give this as 1-n where n is your UMI length. For InDrops, set UMI range to start after the cell barcode (eg. -m 23-28). -l <readlength> : Read length of -r cDNA reads (e.g. 50). Required. -l <readlength> : Read length of -r cDNA reads (e.g. 50). Required. For STRT-seq give this as a total length of your umicdna read. For STRT-seq give this as a total length of your umicdna read. Loading Loading
zUMIs-master.sh +2 −2 Original line number Original line Diff line number Diff line Loading @@ -3,7 +3,7 @@ # Pipeline to run UMI-seq analysis from fastq to read count tables. # Pipeline to run UMI-seq analysis from fastq to read count tables. # Authors: Swati Parekh & Christoph Ziegenhain # Authors: Swati Parekh & Christoph Ziegenhain # Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se or hellmann@bio.lmu.de # Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se or hellmann@bio.lmu.de vers=0.0.6c vers=0.0.6d function check_opts() { function check_opts() { value=$1 value=$1 name=$2 name=$2 Loading Loading @@ -42,7 +42,7 @@ Make sure you have 3-4 times more disk space to your input fastq files. For STRT-seq give this as 1-n where n is your first cell barcode(-f) length. For STRT-seq give this as 1-n where n is your first cell barcode(-f) length. For InDrops give this as 1-n where n is the total length of cell barcode (8bp BC part1 + 6bp library barcode + 8bp BC part2) (e.g. 1-22). For InDrops give this as 1-n where n is the total length of cell barcode (8bp BC part1 + 6bp library barcode + 8bp BC part2) (e.g. 1-22). -m <XM baserange> : Base range for UMI barcode in -f Barcode read(e.g. 7-16). Required. -m <XM baserange> : Base range for UMI barcode in -f Barcode read(e.g. 7-16). Required. For STRT-seq/InDrops give this as 1-n where n is your UMI length. For STRT-seq give this as 1-n where n is your UMI length. For InDrops, set UMI range to start after the cell barcode (eg. -m 23-28). -l <readlength> : Read length of -r cDNA reads (e.g. 50). Required. -l <readlength> : Read length of -r cDNA reads (e.g. 50). Required. For STRT-seq give this as a total length of your umicdna read. For STRT-seq give this as a total length of your umicdna read. Loading
