I suspect the reason articles/papers/etc were saying that you should use Tophat is because it is a spliced read aligner which is a critical feature when aligning RNA-seq reads to a reference genome (Spliced Read Aligner means that it maps reads over exon/intron junctions). There are other aligners which do this too, but bowtie is not one of them (tophat actually uses bowtie to do it's alignment, but that's another story...)

Does BWA map reads over introns? I did a brief search but couldn't find anything to suggest it does. If it does not, you should consider carefully whether it is a good choice. Mapping RNA-seq reads without a way of mapping over junctions will result in exon 'islands' and will not map any read which spans an intron. Unless this really isn't a problem for the aim of your experiment (rare), you should go with a spliced read aligner like Tophat.

Personally, I use Tophat to map RNA-seq reads and BWA to map genomic DNA-derived reads (from ChIPseq).

Does this answer your question?

TopHat is is the most popular mapper for RNA-seq data, but others exist. The RUM paper evaluated several:

• TopHat
• GSNAP
• MapSplice
• SpliceMap
• SoapSplice (listed as Soap/Soapals in the paper)

Other spliced reads aligners exist, you may also try STAR for example that seems to give quite good mappings.

Another splice-aware alignment tools that was recently published is:

CRAC: an integrated approach to the analysis of RNA-seq reads

Provisional abstract: "A large number of RNA-sequencing studies set out to predict mutations, splice junctions or fusion RNAs. We propose a method, CRAC, that integrates genomic locations and local coverage to enable such predictions to be made directly from RNA-seq read analysis. A k-mer profiling approach detects candidate mutations, indels and splice or chimeric junctions in each single read. CRAC increases precision compared with existing tools, reaching 99:5% for splice junctions, without losing sensitivity. Importantly, CRAC predictions improve with read length. In cancer libraries, CRAC recovered 74% of validated fusion RNAs and predicted novel recurrent chimeric junctions. CRAC is available at http://crac.gforge.inria.fr."

Hi, Of course not, SOAP-splice can also do this work. However, Tophat is the most popular software because it can handle gene splice and easy to use. If you use bwa directly, alternative splice will be ignored. If you want to get a higher mapping percentage, you can use some parameters in bowtie, such like --very-sensitive. And tophat2 should be better than tophat. I hope this can help you.

I would recommend RNA-seq blog to you. It traces all publications regarding RNA-seq. You can find most mapping tools there.

Recently, there is a new tool called StringTie, they published the paper in NATURE BIOTECHNOLOGY 18 February 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

In our lab, there are some discussion about StringTie and Tophat. But we haven't made the final decision.