RNAFramework¶

Description¶

RNA Framework is a modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data.

Environment Modules¶

Run module spider rnaframework to find out what environment modules are available for this application.

Environment Variables¶

HPC_RNAFRAMEWORK_DIR - installation directory
HPC_RNAFRAMEWORK_BIN - executable directory

Job Script Examples¶

Job script used for testing application installation:

#!/bin/bash
#SBATCH --job-name=rnaframework_2.7.2_test
#SBATCH --mail-type=NONE
#SBATCH --cpus-per-task=32
#SBATCH --mem-per-cpu=2gb
#SBATCH --time=24:00:00
#SBATCH --output=rnaframework_2.7.2_test.log

echo "Setting up test environment..."
TEST_PWD=/data/apps/tests/rnaframework/2.7.2
TEST_DATADIR=${TEST_PWD}/example_data
TEST_WORKDIR=${TEST_PWD}/test_output

cd ${TEST_PWD}
module load rnaframework/2.7.2

# Remove any previous test results and re-create a working directory
if [ -d ${TEST_WORKDIR} ]; then rm -rf ${TEST_WORKDIR}/; fi
mkdir ${TEST_WORKDIR}

cd ${TEST_WORKDIR}

echo "Starting test run at $(date) on $(hostname)..."

###################################
# echo 'Retrieving reference index...'
# rf-index \
#     --prebuilt 6 \
#     --bowtie2 \
#     --processors ${SLURM_CPUS_ON_NODE:-1}

echo 'Map reads to reference...'
rf-map \
    --bowtie2 \
    --processors ${SLURM_CPUS_ON_NODE:-1} \
    --mapping-params "-D 20 -R 3 -N 0 -L 20 -i S,1,0.50 "\
    --bowtie-index ${TEST_DATADIR}/reference/reference ${TEST_DATADIR}/571-2_S2_L003_R2_001.fastq

echo 'Count RT-stops in both samples...'
rf-count \
    --processors ${SLURM_CPUS_ON_NODE:-1} \
    --fasta ${TEST_DATADIR}/reference/reference.fa \
    rf_map/571-2_S2_L003_R2_001.bam

echo 'Normalize data...'
rf-norm \
    --processors ${SLURM_CPUS_ON_NODE:-1} \
    --scoring-method 4 \
    --raw \
    --treated rf_count/571-2_S2_L003_R2_001.rc

# echo 'Perform inference of secondary structures...'
# rf-fold \
#     --processors ${SLURM_CPUS_ON_NODE:-1} \
#     -img \
#     S1_vs_V1_norm
###################################

# There should be some files in the work directory
echo "There should be some results listed below:"
find ${TEST_WORKDIR}/571-2_S2_L003_R2_001_raw f ! -empty -ls
#find ${TEST_WORKDIR}/rf_fold -type f ! -empty -ls

echo "Test complete at $(date)."

Categories¶

biology, RNA, sequencing