what is the difference between using "NGS:mapping-------Map with
Bowtie for Illumina" and "NGS: RNA analysis---------Tophat for
Illumina" when mapping reads against a reference/custom genome?
Both can be used with a custom reference genome - there is no
between the tools in that regard. However, Bowtie is for mapping DNA
Tophat is for mapping RNA. More details are on the tool forms,
links to the primary tool home pages.
Hopefully this helps,