Objectives
...
| Code Block |
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| title | Get set up for the exercises |
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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:
| Code Block |
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module load biocontainers
module load intel/17.0.4
module load bwa |
...
| Warning |
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| title | Submit to the TACC queue or run in idev session |
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Create a commands file and use launcher_creator.py followed by sbatch. Make sure each command is one line in your commands file. | Code Block |
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| title | Put this in your commands file |
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| nano commands.mem
#Enter these lines into the file
bwa mem -o C1_R1.mem.sam ../reference/transcripts.fasta ../data/GSM794483_C1_R1_1.fq ../data/GSM794483_C1_R1_2.fq
bwa mem -o C1_R2.mem.sam ../reference/transcripts.fasta ../data/GSM794484_C1_R2_1.fq ../data/GSM794484_C1_R2_2.fq
bwa mem -o C1_R3.mem.sam ../reference/transcripts.fasta ../data/GSM794485_C1_R3_1.fq ../data/GSM794485_C1_R3_2.fq
bwa mem -o C2_R1.mem.sam ../reference/transcripts.fasta ../data/GSM794486_C2_R1_1.fq ../data/GSM794486_C2_R1_2.fq
bwa mem -o C2_R2.mem.sam ../reference/transcripts.fasta ../data/GSM794487_C2_R2_1.fq ../data/GSM794487_C2_R2_2.fq
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 |
| Expand |
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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 intel/17.0.4;module load bwa" -l bwa_mem_launcher.slurm |
| Expand |
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| title | Use sbatch to submit your job to the queue |
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| sbatch --reservation=RNAseq bwa_mem_launcher.slurm
#or if reservation is giving us issues sbatch bwa_mem_launcher.slurm |
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Since this will take a while to run, you can look at already generated results at: bwa_mem_results_transcriptome
Alternatively, we can also use bwa to map to the genome (reference/genome.fa).
Now that we are done mapping, lets look at how to assess mapping results.