Objectives
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Submit to the TACC queue or run in an idev shellCreate a commands file and use launcher_creator.py followed by sbatch. Put this in your commands file| Code Block |
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nano commands.quant
singularity exec ${BIOCONTAINER_DIR}/biocontainers/kallisto/kallisto-0.45.0--hdcc98e5_0.simg kallisto quant -i ../reference/transcripts.idx -b 100 -o GSM794483_kallisto ../data/GSM794483_C1_R1_1.fq ../data/GSM794483_C1_R1_2.fq 2>GSM794483_kallisto
singularity exec ${BIOCONTAINER_DIR}/biocontainers/kallisto/kallisto-0.45.0--hdcc98e5_0.simg kallisto quant -i ../reference/transcripts.idx -b 100 -o GSM794484_kallisto ../data/GSM794484_C1_R2_1.fq ../data/GSM794484_C1_R2_2.fq 2>GSM794484_kallisto
singularity exec ${BIOCONTAINER_DIR}/biocontainers/kallisto/kallisto-0.45.0--hdcc98e5_0.simg kallisto quant -i ../reference/transcripts.idx -b 100 -o GSM794485_kallisto ../data/GSM794485_C1_R3_1.fq ../data/GSM794485_C1_R3_2.fq 2>GSM794485_kallisto
singularity exec ${BIOCONTAINER_DIR}/biocontainers/kallisto/kallisto-0.45.0--hdcc98e5_0.simg kallisto quant -i ../reference/transcripts.idx -b 100 -o GSM794486_kallisto ../data/GSM794486_C2_R1_1.fq ../data/GSM794486_C2_R1_2.fq 2>GSM794486_kallisto
singularity exec ${BIOCONTAINER_DIR}/biocontainers/kallisto/kallisto-0.45.0--hdcc98e5_0.simg kallisto quant -i ../reference/transcripts.idx -b 100 -o GSM794487_kallisto ../data/GSM794487_C2_R2_1.fq ../data/GSM794487_C2_R2_2.fq 2>GSM794487_kallisto
singularity exec ${BIOCONTAINER_DIR}/biocontainers/kallisto/kallisto-0.45.0--hdcc98e5_0.simg kallisto quant -i ../reference/transcripts.idx -b 100 -o GSM794488_kallisto ../data/GSM794488_C2_R3_1.fq ../data/GSM794488_C2_R3_2.fq fq 2>GSM794488_kallisto |
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| title | Use this Launcher_creator command |
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| launcher_creator.py -n kallisto -t 01:00:00 -j commands.quant -q normal -a OTH21164 -l kallisto_launcher.slurm -m "module load biocontainers;module load kallisto" |
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| sbatch --reservation=rna-seq-class-0610 kallisto_launcher.slurm |
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Output files:
abundances.tsv: A tsv file containing raw read count and a normalized expression value for each transcript.
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