Objectives
In this lab, you will explore a faster splice aware mapper called STAR. Simulated RNA-seq data will be provided to you; the data contains 75 bp paired-end reads that have been generated in silico to replicate real gene count data from Drosophila. The data simulates two biological groups with three biological replicates per group (6 samples total). The objectives of this lab is mainly to:
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module spider star
#if not already loaded, module load biocontainers
module load star |
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#get the full path to STAR
type STAR
#the below command would need to be RUN IN AN IDEV SESSION since you cannot run biocontainer executables on login nodes.
STAR --help |
Part 1. Create a index of your reference
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| title | Submit to the TACC queue or run in an idev shell |
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Create a commands file and use launcher_creator.py followed by sbatch. | Expand |
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nano commands.star
Put this in your commands file: apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b--h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C1_R1 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794483_C1_R1_1.fq ../data/GSM794483_C1_R1_2.fq apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b--h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C1_R2 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794484_C1_R2_1.fq ../data/GSM794484_C1_R2_2.fq apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b--h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C1_R3 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794485_C1_R3_1.fq ../data/GSM794485_C1_R3_2.fq apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b--h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C2_R1 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794486_C2_R1_1.fq ../data/GSM794486_C2_R1_2.fq apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b–h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C2_R2 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794487_C2_R2_1.fq ../data/GSM794487_C2_R2_2.fq apptainer exec ${BIOCONTAINER_DIR}/biocontainers/star/star-2.7.11b–h43eeafb_1.sif STAR --runThreadN 1 --outFileNamePrefix C2_R3 --outSAMstrandField intronMotif --genomeDir ../reference/STAR_genome --outSAMtype BAM Unsorted --readFilesIn ../data/GSM794488_C2_R3_1.fq ../data/GSM794488_C2_R3_2.fq |
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| title | Use this Launcher_creator command |
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| launcher_creator.py -j commands.star -n starmap -q normal -t 08:00:00 -a OTH21164 -l star_launcher.slurm -m "module load biocontainers; module load star" -N 6 -w 1 |
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| sbatch --reservation=RNAseq star_launcher.slurm |
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This brings up the concept of wayness when running things on lonestar6! Let's go back to Submitting Jobs to lonestar6 to discuss that.
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