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There are lots of options, but here is a summary of the most important ones. BWA, is a lot more complex than the options let on. If you look at the BWA manual on the web for the aln sub-command, you'll see numerous options that can increase the alignment rate (as well as decrease it), and all sorts of other things.
| Option | Effect |
|---|---|
| -kl | Controls the number length of mismatches allowable in the seed of each alignment (default = 232) |
| -lk | Controls the length number of mismatches allowable in the seed of each alignment (default = 322) |
| -n | Controls the number of mismatches (or fraction of bases in a given alignment that can be mismatches) in the entire alignment (including the seed) (default = 0.04) |
| -t | Controls the number of threads |
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| There are 1184360 alignment records. |
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Exercise: How many sequences were in the R1 and R2 FASTQ files combined?
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| There were a total of 1184360 original sequences |
Exercises:
- Do both R1 and R2 reads have separate alignment records?
- Does the SAM file contain both aligned and un-aligned reads?
- What is the order of the alignment records in this SAM file?
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Exercise #2: Bowtie2 and Local Alignment - Human microRNA-seq
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