UPPMAX

Run on UPPMAX

Installation

git clone -b v3dev https://github.com/shka/STRTprep.git STRTprep3.test
cd STRTprep3.test
bin/install_uppmax.sh

Protocol

• Step 1: (Copy pre-build indexes, or) build indexes of reference genome and transcriptome, like as

sbatch -A bXXXXXXX -t 12:00:00 -p core -n 1 <<EOF
#!/usr/bin/env bash
. bin/setup_uppmax.sh
bin/index_hg19_ercc92_ynbA_u13369.sh
bin/index_refGene.sh hg19 src/ebwt/hg19_ercc92_ynbA_u13369/ref
EOF

• Step 2: Edit conf.yaml and src/samples.csv
• Step 3: Run preprocessing and quality-check as follows, then check out/byGene/samples.xls

sbatch -A bXXXXXXX -t 24:00:00 -p node -n 16 <<EOF
#!/usr/bin/env bash
. bin/setup_uppmax.sh
rake -m -j 16 qc
EOF

• Step 4: Run differential expression tests as follows, then check out/byGene/diffexp.xls and analyze more further!

sbatch -A bXXXXXXX -t 24:00:00 -p node -n 16 <<EOF
#!/usr/bin/env bash
. bin/setup_uppmax.sh
rake gene
EOF

• [v3dev] Step 5: Add "CLASS.TFE" column for classification of samples into src/samples.csv table, run differential expression tests, based on transcription-start-regions, then check out/byTFE/diffexp.xls and analyze more further!

sbatch -A bXXXXXXX -t 24:00:00 -p node -n 16 <<EOF
#!/usr/bin/env bash
. bin/setup_uppmax.sh
rake
EOF

• Tips: If the job will finish within one hour (ex. addition of one differential expression test, update of plugins without new differential expression tests, and so on), you can use devel queue instead of node, which can run a job up to one hour for development/test purpose. For example,

sbatch -A bXXXXXXX -t 1:00:00 -p devel -n 16 <<EOF
#!/usr/bin/env bash
. bin/setup_uppmax.sh
rake gene
EOF