added master template

dge_workflow/dge_master.sh

+export baseDir=<<PATH_TO_BASEDIR>>
+export project=<<PROJECTNAME>>
+
+screen -R $project
+
+########################################################################################################################
+### Setup
+
+## change if you want to use customized copy
+DGE_HOME=/projects/bioinfo/holger/bioinfo_templates/dge_workflow
+
+
+source <(curl https://dl.dropboxusercontent.com/u/113630701/datautils/bash/lsf_utils.sh 2>&1 2>/dev/null)
+source <(curl https://dl.dropboxusercontent.com/u/113630701/datautils/R/utils/spinr.sh 2>&1 2>/dev/null)
+source $DGE_HOME/lsf_rna_seq.sh
+
+
+export PATH=/projects/bioinfo/holger/bin/bowtie2-2.2.2:$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
+# which tophat;  which bowtie2; which cuffdiff
+
+
+########################################################################################################################
+#### QC
+
+
+#fastqFiles=$(ls /projects/bioinfo/holger/projects/helin/all_trep_pooled/dog_*)
+fastqFiles=<<TBD>>
+#ll $fastqFiles
+
+## do some qc for the reads
+dge_fastqc -o $baseDir/fastqc $fastqFiles &
+
+## create a fastqc report
+spinr $DGE_HOME
+
+mailme "$project: fastqc done"
+
+
+########################################################################################################################
+### Map the data and do cuffdiff
+
+mcdir $baseDir/mapped
+
+#igenome=/projects/bioinfo/igenomes/Canis_familiaris/Ensembl/CanFam3.1
+igenome=<<TBD>>
+
+
+dge_tophat_se -i $igenome $fastqFiles 2>&1 | tee mapped.log
+
+mailme "$project: mapping done"
+
+
+########################################################################################################################
+### Do the differential expression analysis
+
+mcdir $baseDir/cuffdiff
+
+gtfFile=$igenome/Annotation/Genes/genes.gtf
+
+## define labels to split bam files into replicate groups
+#labels="big_cyst,small_cyst"
+labels=<<TBD>>
+
+dge_cuffdiff $gtfFile $baseDir/mapped $labels
+MakeCuffDB $gtfFile "NAN"
+
+mailme "$project: cuffdiff done"
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