6 months ago by
From the tool documentation:
--strata Best strata. When running in best mode, report alignments that fall into the
best stratum if there are ones falling into more than one. [off]
With full details here: http://bowtie-bio.sourceforge.net/manual.shtml#strata
strata filter will limit the hits reported, per query sequence, to the "best". There can be more than one "best hit" for some cases as described in the link above.
If the goal is to only report one alignment per query sequence, try the option
Report up to n valid alignments per read (-k) set at
1. Please be aware that you may miss important hits using this method. For this job, this option was left at default (report all alignments that meet other set criteria).
There are other ways to filter the output, both during alignment and after (Galaxy has several BAM filter tools wrapped and available at the public server http://usegalaxy.org). You might want to review the choices for alignment and post-alignment filtering, test a few out, compare the results, and then determine the optimal settings/workflow for your project. See the examples of Bowtie (version 1) parameter combinations and the results produced by each in the manual link above to better understand how options work together.
All of this said, moving to the updated version of the tool, Bowtie2, is strongly recommended. Tools and tool wrappers change over time as bug fixes are made (to either) and new features/options are introduced or removed. The Bowtie2 manual can be found here: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml. Please note this change related to the concept of grouping/scoring alignments by "stratum":
Bowtie 2 does away with Bowtie 1's notion of alignment "stratum", and
its distinction between "Maq-like" and "end-to-end" modes. In Bowtie 2
all alignments lie along a continuous spectrum of alignment scores
where the scoring scheme, similar to Needleman-Wunsch and
For reference, Galaxy tutorials covering common analysis workflows can be found here: https://galaxyproject.org/learn/
Hopefully, this helps you decide how to proceed! Jen, Galaxy team