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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 qsub.

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

Put this in your commands file:

Code Block
bwa sampe -f bwa/SRR030257.sam bwa/NC_012967.1.fasta bwa/SRR030257_1.sai bwa/SRR030257_2.sai SRR030257_1.fastq SRR030257_2.fastq

 

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

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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 qsub.

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

Put this in your commands file:

Code Block
bwa mem

Assessing Mapping Results

 

 

 

run BWA pipeline