...
You did it! In the alignments directory, there should exist the two intermediate files (the SAI files), along with the SAM file that contains the alignments. It's just a text file, so take a look with head, more, less, tail, or whatever you feel like. In the next section, with samtools, you'll learn some additional ways to analyze the data. BWA, however, is a lot more complex than the above commands let on. If you look at the help pages for 'bwa aln' in particluar, there are numerous options that can increase the alignment rate (as well as decrease it), and all sorts of other things. There are lots of options, but here is a summary of the most important ones.
| Option | EffectBest Practice Setting | |||||
|---|---|---|---|---|---|---|
| -k | Controls the number of mismatches allowable in the seed of each alignment (default = 2) | |||||
| -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) | |||||
| -l | Controls the length of the seed (default = 32) | -l | ||||
| -t | Controls the number of threads |
The rest of the options control the details of how much a mismatch or gap is penalized, limits on the number of acceptable hits per read, and so on. Much more information can be accessed at the BWA manual page.
Exercise #2: Bowtie2 and Local Alignment - Human microRNA-seq
...