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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
titleclick here for a hint before getting the answer

 

launcher_creator.py -h will give you insight to how to use that command.

Code Block
languagebash
titleClick here for the specific launcher_creator.py commands
collapsetrue
launcher_creator.py -n "bowtie2" --time 00:10:00
Code Block
languagebash
titlecommands for the commands file if you can't work them out yourself
collapsetrue
bowtie2 -t -x bowtie2/NC_012967.1 -1 SRR030257_1.fastq -2 SRR030257_2.fastq -S bowtie2/SRR030257.sam  # the -t command is not required for the mapping, but it can be particularly informative when you begin comparing different mappers
Code Block
languagebash
titleClick here for the specific launcher_creator.py commands
collapsetrue
launcher_creator.py -n "bowtie2" -t 00:10:00

 

 

 

 

Your final output file is in SAM format. It's just a text file, so you can peek at it and see what it's like inside. Two warnings though:

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Expand
titleWhat do you think the 4th and 8th columns mean(click for answer)?
What do you think the 4th and 8th columns mean?If you thought the answer was the mapping coordinates of the read pairs you were right!

More reading about SAM files

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  • In the bowtie2 example, we mapped in --local mode. Try mapping in --end-to-end mode (aka global mode).

  • Do the BWA tutorial so you can compare their outputs.
    • Did bowtie2 or BWA map more reads?
    • In our examples, we mapped in paired-end mode. Try to figure out how to map the reads in single-end mode and create this output.
    • Which aligner took less time to run? Are there any options you can change that:
      • Lead to a larger percentage of the reads being mapped? (increase sensitivity)
      • Speed up performance without causing many fewer reads to be mapped? (increase performance)

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