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Dhivya Arasappan

Dhivya Arasappan

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Warning
titleSubmit to the TACC queue or run in an idev shell

Create a commands file and use launcher_creator.py followed by sbatch.

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nano commands.bwa

 

Put this in your commands file:

bwa aln -f GSM794483_C1_R1_1.sai reference/genome.fa data/GSM794483_C1_R1_1.fq

bwa aln -f GSM794483_C1_R1_2.sai reference/genome.fa data/GSM794483_C1_R1_2.fq

bwa aln -f GSM794484_C1_R2_1.sai reference/genome.fa data/GSM794484_C1_R2_1.fq

bwa aln -f GSM794484_C1_R2_2.sai reference/genome.fa data/GSM794484_C1_R2_2.fq

bwa aln -f GSM794485_C1_R3_1.sai reference/genome.fa data/GSM794485_C1_R3_1.fq

bwa aln -f GSM794485_C1_R3_2.sai reference/genome.fa data/GSM794485_C1_R3_2.fq

bwa aln -f GSM794486_C2_R1_1.sai reference/genome.fa data/GSM794486_C2_R1_1.fq

bwa aln -f GSM794486_C2_R1_2.sai reference/genome.fa data/GSM794486_C2_R1_2.fq

bwa aln -f GSM794487_C2_R2_1.sai reference/genome.fa data/GSM794487_C2_R2_1.fq

bwa aln -f GSM794487_C2_R2_2.sai reference/genome.fa data/GSM794487_C2_R2_2.fq

bwa aln -f GSM794488_C2_R3_1.sai reference/genome.fa data/GSM794488_C2_R3_1.fq

bwa aln -f GSM794488_C2_R3_2.sai reference/genome.fa data/GSM794488_C2_R3_2.fq

 

Expand
titleUse this Launcher_creator command

launcher_creator.py -n aln -t 04:00:00 -j commands.bwa -q normal -a CCBB UT-2015-05-18 -m "module load bwa/0.7.7" -l bwa_launcher.slurm

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Warning
titleSubmit to the TACC queue or run in an idev shell

Create a commands file and use launcher_creator.py followed by sbatch.

Expand
titleI need some help figuring out the options...

nano commands.bwa.sampe

 

Put this in your commands file:

bwa sampe -f C1_R1.sam reference/genome.fa GSM794483_C1_R1_1.sai GSM794483_C1_R1_2.sai data/GSM794483_C1_R1_1.fq data/GSM794483_C1_R1_2.fq

bwa sampe -f C1_R2.sam reference/genome.fa GSM794484_C1_R2_1.sai GSM794484_C1_R2_2.sai data/GSM794484_C1_R2_1.fq data/GSM794484_C1_R2_2.fq

bwa sampe -f C1_R3.sam reference/genome.fa GSM794485_C1_R3_1.sai GSM794485_C1_R3_2.sai data/GSM794485_C1_R3_1.fq data/GSM794485_C1_R3_2.fq

bwa sampe -f C2_R1.sam reference/genome.fa GSM794486_C2_R1_1.sai GSM794486_C2_R1_2.sai data/GSM794486_C2_R1_1.fq data/GSM794486_C2_R1_2.fq

bwa sampe -f C2_R2.sam reference/genome.fa GSM794487_C2_R2_1.sai GSM794487_C2_R2_2.sai data/GSM794487_C2_R2_1.fq data/GSM794487_C2_R2_2.fq

bwa sampe -f C2_R3.sam reference/genome.fa GSM794488_C2_R3_1.sai GSM794488_C2_R3_2.sai data/GSM794488_C2_R3_1.fq data/GSM794488_C2_R3_2.fq

Expand
titleUse this Launcher_creator command

launcher_creator.py -n sampe -t 04:00:00 -j commands.bwa.sampe -q normal -a UT-2015-05-18 -m "module load bwa/0.7.7" -l bwa_sampe_launcher.slurm

sbatch --dependency=afterok:<aln-job-ID> bwa_sampe_launcher.slurm


Part 2b. Align the samples to reference using bwa mem

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