2 answers
Why do you want to do that ?. It is non sense..
TopHat will do a initial mapping using bowtie2 (so you get the same that using bowtie2 alone), and it will do a segmentation of the unmapped sequences to try a new mapping using bowtie2 again to detect spliced sequences
Tophat2 will give them a MAPQ or 0, 1, 2, or 3. Non-multimappers are given a MAPQ of 50 (last time I looked at least).
Take a look to this page
Inside the SAM file, you can read a FLAG value which is interpreted by the page shown above. It will be useful for you
If you have a sam/bam file, you can compare which mapping tool could align more number of reads. properly and improperly paired reads and overall number of reads aligned would help you.
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hello,
what version of bowtie you used in tophat? and what version of tophat you have used?
bowtie2 and tophat2