Presets: setting many settings at once
"Bowtie 2 comes with some useful combinations of parameters packaged into shorter "preset" parameters. For example, running Bowtie 2 with the --very-sensitive option is the same as running with options: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50."
Default mode: search for multiple alignments, report the best one
By default, Bowtie 2 searches for distinct, valid alignments for each read. When it finds a valid alignment, it generally will continue to look for alignments that are nearly as good or better. It will eventually stop looking, either because it exceeded a limit placed on search effort (see -D and -R) or because it already knows all it needs to know to report an alignment. Information from the best alignments are used to estimate mapping quality (the MAPQ SAM field) and to set SAM optional fields, such as AS:i and XS:i. Bowtie 2 does not gaurantee that the alignment reported is the best possible in terms of alignment score.
The sensitivity does not influence the reporting (directly). By default bowtie2 reports one alignment.
B) SAM is a published specification in which alignments can be reported. The benefit is that more and more downstream tools (e.g. GATK, MACS, genome browsers) directly accept this as input. Actually its most of the time sorted and indexed BAM - which is the binary aequivalent of SAM -, so you might have to put in more effort, but bam conversion and sorting can be done by piping.
modified 7.7 years ago
7.7 years ago by
Ido Tamir ♦ 5.0k