For RNA-seq analysis, removing any reads would be problematic since
would interfere with expression/abundance calculations. For mapping,
TopHat is the preferred alignment tool for spliced RNA data. BWA and
Bowtie are tools better suited for DNA mapping.
For Prokaryote genomes, the choice of which alignment tool to use may
more flexible (splicing would not be an issue), but understanding the
parameters for the tool options and how to tune appropriately (e.g.
a circular genome) would be important to research and test out.
For more details about TopHat, please see the author's web site
(including an FAQ) at: http://tophat.cbcb.umd.edu/. A help email is
Trimming is a different operation than removing sequences and could be
applied to both RNA and DNA data. Unfortunately, there are no
generalized rules that could be applied to all cases.
The type of data and the mapping tool will determine if trimming is
needed and when it should be done.
Some mappers have quality trimming options in the tool form itself
example, Bowtie, in the full parameter list).
These screencasts may help, as would the target mapping tool
see: Basic FASTQ Manipulation
Advanced FASTQ Manipulation
For next time, please continue to send questions with the "to" address
as the mailing list and replies as "reply-all, it helps us greatly
If anyone else on the mailing list has more help to offer, they are
welcome to jump in on the discussion. Although, you would likely need
post to the mailing list the source/format of your query data and
tool you are considering using in order to receive specific advice.