diff --git a/dge_workflow/dge_utils.sh b/dge_workflow/dge_utils.sh index d82dfe83df7a332470d3a44ebc9eee04fc79a35c..2a8f67c0b242fe18c1a1c38dd6c955675919fffe 100755 --- a/dge_workflow/dge_utils.sh +++ b/dge_workflow/dge_utils.sh @@ -5,11 +5,11 @@ #source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/bash/lsf_utils.sh 2>&1 2>/dev/null) ## enable snippet spinning -source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/spinr/spin_utils.sh 2>&1 2>/dev/null) -export PATH=/home/brandl/bin/spinr:$PATH +source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/spinr/spin_utils.sh 2>&1 2>/dev/null) +export PATH=/projects/bioinfo/holger/bin//spinr:$PATH source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/rendr/rendr_utils.sh 2>&1 2>/dev/null) -export PATH=/home/brandl/bin/rendr:$PATH +export PATH=/projects/bioinfo/holger/bin//rendr:$PATH ## define common binaries @@ -18,7 +18,7 @@ export PATH=/projects/bioinfo/holger/bin/bowtie2-2.2.5:$PATH export PATH=/projects/bioinfo/holger/bin/tophat-2.0.13.Linux_x86_64:$PATH export PATH=/home/brandl/bin/cufflinks-2.2.1.Linux_x86_64:$PATH export PATH=/sw/apps/python/current/bin:$PATH -export PATH=/home/brandl/bin/deepTools/bin:$PATH +export PATH=/projects/bioinfo/holger/bin/deepTools/bin:$PATH export PATH=/projects/bioinfo/holger/bin/FastQC_0.11.2:$PATH export PATH=/projects/bioinfo/holger/bin/bedtools2-2.25.0/bin/:$PATH export PATH=/projects/bioinfo/holger/bin/samtools-1.3:$PATH diff --git a/dge_workflow/featcounts_deseq.R b/dge_workflow/featcounts_deseq.R index 157c0a7f0a8eb6b8eb42398e3e70538e9e5fcc77..4926141a42cc3488efac4d70fb2186f825c7ff59 100755 --- a/dge_workflow/featcounts_deseq.R +++ b/dge_workflow/featcounts_deseq.R @@ -126,8 +126,8 @@ if(!all((contrasts %>% gather %$% value %>% unique) %in% colData$condition)){ #stopifnot(all((contrasts %>% gather %$% value %>% unique) %in% colData$condition)) dds <- DESeqDataSetFromMatrix(countMatrix, colData, formula(~ condition)) -dds <- estimateSizeFactors(dds) -dds <- estimateDispersions(dds) +#dds <- estimateSizeFactors(dds) +#dds <- estimateDispersions(dds) ########################################################################################################################