Tophat: Can I forbid splice junction?
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?
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Please read the message at the top of the TopHat page: http://ccb.jhu.edu/software/tophat/index.shtml
In addition to HISAT2, also STAR and bbmap are good choices.