Tophat: Can I forbid splice junction?

Question

[--panda--]

I'm working on bacteria data and in such data there is no need to discover splice junction.

I knew the fact that Tophat is design for splice junction detect and it's build on the bowtie2 index and aligning algorithm.Technically, using bowtie2 solves my problem.

But I do like the fact that Tophat has a more complete alignment report and the automatic sort and compress function.

So as the post title says: anyway to turn off the splice junction when do alignment?

[WouterDeCoster]

Please read the message at the top of the TopHat page: http://ccb.jhu.edu/software/tophat/index.shtml

TopHat 2.1.1 release 2/23/2016 Please note that TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2 which provides the same core functionality (i.e. spliced alignment of RNA-Seq reads), in a more accurate and much more efficient way.

In addition to HISAT2, also STAR and bbmap are good choices.