Objectives
In this lab, you will explore a popular fast mapper called BWA. 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:
Introduction
BWA (the Burrows-Wheeler Aligner) is a fast short read aligner. It is an unspliced mapper. As the name suggests, it uses the burrows-wheeler transform to perform alignment in a time and memory efficient manner.
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ls ../data
ls ../reference
#transcriptome
head ../reference/transcripts.fasta
#see how many transcripts there are in the file
grep -c '^>' ../reference/transcripts.fasta
#genome
head ../reference/genome.fa
#see how many sequences there are in the file
grep -c '^>' ../reference/genome.fa
#annotation
head ../reference/genes.formatted.gtf
#see how many entries there are in this file
wc -l ../reference/genes.formatted.gtf |
Run BWA
Load the module:
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module load biocontainers
module load bwa
#to get the full path for bwa
type bwa |
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Submit to the TACC queue or run in idev sessionCreate a commands file and use launcher_creator.py followed by sbatch. Make sure each command is one line in your commands file. Put this in your commands file| Code Block |
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nano commands.mem
#Enter these lines into the file
singularity exec ${BIOCONTAINER_DIR}/biocontainers/bwa/bwa-0.7.17--pl5.22.0_2.simg bwa mem -o C1_R1.mem.sam ../reference/transcripts.fasta ../data/GSM794483_C1_R1_1.fq ../data/GSM794483_C1_R1_2.fq
singularity exec ${BIOCONTAINER_DIR}/biocontainers/bwa/bwa-0.7.17--pl5.22.0_2.simg bwa mem -o C1_R2.mem.sam ../reference/transcripts.fasta ../data/GSM794484_C1_R2_1.fq ../data/GSM794484_C1_R2_2.fq
singularity exec ${BIOCONTAINER_DIR}/biocontainers/bwa/bwa-0.7.17--pl5.22.0_2.simg bwa mem -o C1_R3.mem.sam ../reference/transcripts.fasta ../data/GSM794485_C1_R3_1.fq ../data/GSM794485_C1_R3_2.fq
singularity exec ${BIOCONTAINER_DIR}/biocontainers/bwa/bwa-0.7.17--pl5.22.0_2.simg bwa mem -o C2_R1.mem.sam ../reference/transcripts.fasta ../data/GSM794486_C2_R1_1.fq ../data/GSM794486_C2_R1_2.fq
singularity exec ${BIOCONTAINER_DIR}/biocontainers/bwa/bwa-0.7.17--pl5.22.0_2.simg bwa mem -o C2_R2.mem.sam ../reference/transcripts.fasta ../data/GSM794487_C2_R2_1.fq ../data/GSM794487_C2_R2_2.fq
singularity exec ${BIOCONTAINER_DIR}/biocontainers/bwa/bwa-0.7.17--pl5.22.0_2.simg bwa mem -o C2_R3.mem.sam ../reference/transcripts.fasta ../data/GSM794488_C2_R3_1.fq ../data/GSM794488_C2_R3_2.fq
#ctrl+X to exit nano
#Y, followed by enter to save file |
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| title | Use this Launcher_creator command |
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| launcher_creator.py -n mem -t 04:00:00 -j commands.mem -q normal -a OTH21164 -m "module load biocontainers;module load bwa" -l bwa_mem_launcher.slurm |
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| title | Use sbatch to submit your job to the queue |
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| sbatch --reservation=rna-seq-class-0610 bwa_mem_launcher.slurm #or if reservation is giving us issues sbatch bwa_mem_launcher.slurm |
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