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 below. See also a help document.

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
  • Time of job allocation for (i; 6.5 hours) is an example for a project with three HiSeq lanes for one library. Change in case of larger project; approximately 125 min * lanes
  • Please put job number of (i) into X at (ii); then the latter job will run if the former job succeeded.
  • Time of job allocation for (ii; 1.5 hour) is an example for a project with three HiSeq lanes for one library. Change in case of larger project; approximately 30 min * lanes

sbatch -A b2014069 -t 06:30:00 -p core -n 1 <<EOF ## (i)
#!/usr/bin/env bash
. bin/setup_uppmax.sh
PROCS=16 rake tmp/step2b.trace
EOF
sbatch -A b2014069 -t 01:30:00 -p node -n 16 -d afterok:X <<EOF ## (ii)
#!/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!
  • Please extend time of job allocation (one hour), and change name of queue (devcore to core), when you met timeout
  • Please extend number of CPU allocation (one) when you met memory overflow

sbatch -A b2014069 -t 1:00:00 -p devcore -n 1 <<EOF
#!/usr/bin/env bash
. bin/setup_uppmax.sh
PROCS=16 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 b2014069 -t 24:00:00 -p node -n 16 <<EOF
#!/usr/bin/env bash
. bin/setup_uppmax.sh
rake -m -j 16
EOF