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This command can take a while (~5 minutes) and is extremely taxing. This is longer than we want to run a job on the head node (especially when all of us are doing it at once). In fact, in previous years, TACC has noticed the spike in usage when multiple students forgot to make sure they were on idev nodes and complained pretty forcefully to us about it. Let's not have this be one of those years. Use the
If you are not sure if you are on an idev node or are seeing other output with one or both commands, speak up on zoom and I'll show(q) -u what you are looking for. Yes, your instructor likes bad puns. My apologies. If you are not on an idev node, and need help to relaunch it, click over to the idev tutorial. |
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In the bowtie2 example, we mapped in
--localmode. Try mapping in--end-to-endmode (aka global mode).- Do the BWA tutorial so you can compare their outputs (note BWA has a conda package making it even easier to try).
- 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 run time without causing many fewer reads to be mapped? (increase performance)
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