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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"