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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.

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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

 

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titleUse this Launcher_creator command

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

 *.sai file is a file containing "alignment seeds" in a file format specific to BWA.  We still need to extend these seed matches into alignments of entire reads, choose the best matches, and convert the output to SAM format. Do we use sampe or samse?

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