Loading fqfilter.pl +5 −0 Original line number Diff line number Diff line Loading @@ -160,5 +160,10 @@ if($pbcread ne "NA") { print "Raw reads: $total \nFiltered reads: $filtered \n\n"; $RAM=11330+$filtered*0.000192; $RAM=int($RAM); print "Make sure you have approximately $RAM Mb RAM available"; `$pigz -f -p $threads $cdnareadout`; `$pigz -f -p $threads $bcreadoutfull`; preprocess_splitseq.pl 100644 → 100755 +0 −0 File mode changed from 100644 to 100755. View file zUMIs-dge.R +2 −2 Original line number Diff line number Diff line Loading @@ -33,8 +33,8 @@ option_list = list( help="End position of UMI barcode in the read", metavar="integer"), make_option(c("--subsamp"), type="character", default="0", help="Number of reads for downsampling.", metavar="character"), make_option(c("--nReadsBC"), type="character", default="100", help="Retain cells with atleast N reads.", metavar="character"), make_option(c("--nReadsBC"), type="integer", default="100", help="Retain cells with atleast N reads.", metavar="integer"), make_option(c("--hamming"), type="character", default=0, help="Hamming distance filter", metavar="integer"), make_option(c("--XCbin"), type="character", default=0, Loading zUMIs-master.sh +2 −2 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 # Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se or hellmann@bio.lmu.de vers=0.0.6b vers=0.0.6c function check_opts() { value=$1 name=$2 Loading Loading @@ -57,7 +57,7 @@ Make sure you have 3-4 times more disk space to your input fastq files. defined barcodes as a text file with a list of barcodes without headers (e.g. ATGCCAAT). Default: Adaptive cell barcode selection We highly reccomend to provide expected number of barcodes for Drop-seq protocol. -N <nReadsperCell> : Keep the cell barcodes with atleast "-N <int>" number of reads. Default: 100 Cells with less than "-N <int>" number of total reads are removed. Cells with less than "-N <int>" number of total reads are removed. Only considered in automatic cell barcode selection. -d <downsampling> : Number of reads to downsample to. This value can be a fixed number of reads (e.g. 10000) or a desired range (e.g. 10000-20000). Barcodes with less than <d> will not be reported. 0 means adaptive downsampling. Default: 0. -x <STARparams> : Additional STAR mapping parameters. Optional. e.g. "--outFilterMismatchNoverLmax 0.2 --quantMode TranscriptomeSAM". Loading Loading
fqfilter.pl +5 −0 Original line number Diff line number Diff line Loading @@ -160,5 +160,10 @@ if($pbcread ne "NA") { print "Raw reads: $total \nFiltered reads: $filtered \n\n"; $RAM=11330+$filtered*0.000192; $RAM=int($RAM); print "Make sure you have approximately $RAM Mb RAM available"; `$pigz -f -p $threads $cdnareadout`; `$pigz -f -p $threads $bcreadoutfull`;
zUMIs-dge.R +2 −2 Original line number Diff line number Diff line Loading @@ -33,8 +33,8 @@ option_list = list( help="End position of UMI barcode in the read", metavar="integer"), make_option(c("--subsamp"), type="character", default="0", help="Number of reads for downsampling.", metavar="character"), make_option(c("--nReadsBC"), type="character", default="100", help="Retain cells with atleast N reads.", metavar="character"), make_option(c("--nReadsBC"), type="integer", default="100", help="Retain cells with atleast N reads.", metavar="integer"), make_option(c("--hamming"), type="character", default=0, help="Hamming distance filter", metavar="integer"), make_option(c("--XCbin"), type="character", default=0, Loading
zUMIs-master.sh +2 −2 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 # Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se or hellmann@bio.lmu.de vers=0.0.6b vers=0.0.6c function check_opts() { value=$1 name=$2 Loading Loading @@ -57,7 +57,7 @@ Make sure you have 3-4 times more disk space to your input fastq files. defined barcodes as a text file with a list of barcodes without headers (e.g. ATGCCAAT). Default: Adaptive cell barcode selection We highly reccomend to provide expected number of barcodes for Drop-seq protocol. -N <nReadsperCell> : Keep the cell barcodes with atleast "-N <int>" number of reads. Default: 100 Cells with less than "-N <int>" number of total reads are removed. Cells with less than "-N <int>" number of total reads are removed. Only considered in automatic cell barcode selection. -d <downsampling> : Number of reads to downsample to. This value can be a fixed number of reads (e.g. 10000) or a desired range (e.g. 10000-20000). Barcodes with less than <d> will not be reported. 0 means adaptive downsampling. Default: 0. -x <STARparams> : Additional STAR mapping parameters. Optional. e.g. "--outFilterMismatchNoverLmax 0.2 --quantMode TranscriptomeSAM". Loading
