Content Comparison

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module load bowtie
bowtie-build NC_017544.1.fasta NC_017544.1

bowtie -p 3 -S NC_017544.1 SRR034450.fastq -S SRR034450.sam
bowtie -p 3 -S NC_017544.1 SRR034451.fastq -S SRR034451.sam
bowtie -p 3 -S NC_017544.1 SRR034452.fastq -S SRR034452.sam
bowtie -p 3 -S NC_017544.1 SRR034453.fastq -S SRR034453.sam

module load python
launcher_creator.py -n bowtie -q development -c bowtie_commands -t 0:30:00
qsub bowtie.sge

Convert Bowtie output to BAM

Create a new samtools_commands file so that you convert all of these files from SAM to sorted and indexed BAM all at one time by using qsub.

Linux expert tip: you can string together commands all on one line, so that they are sent to the same core one after another by separating them on the line with &&.

Note the use of the variable $FILE, by which we set a variable's value int he first part of the line and use it over and over in the latter part of the line. This is a mini use of shell scripting.

FILE=SRR034450 && samtools import NC_017544.1.fasta $FILE.sam $FILE.unsorted.bam && samtools sort $FILE.unsorted.bam $FILE && samtools index $FILE.bam
FILE=SRR034451 && samtools import NC_017544.1.fasta $FILE.sam $FILE.unsorted.bam && samtools sort $FILE.unsorted.bam $FILE && samtools index $FILE.bam
FILE=SRR034452 && samtools import NC_017544.1.fasta $FILE.sam $FILE.unsorted.bam && samtools sort $FILE.unsorted.bam $FILE && samtools index $FILE.bam
FILE=SRR034453 && samtools import NC_017544.1.fasta $FILE.sam $FILE.unsorted.bam && samtools sort $FILE.unsorted.bam $FILE && samtools index $FILE.bam

Create a new launcher script and submit this new job to the queue. Be sure you have samtools loaded as the node that your job launches on will inherit your current environment, including whatever modules you have loaded:

module load samtools

launcher_creator.py -n samtools -q development -j samtools_commands -t 0:30:00
qsub samtools.sge

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