bowtie advantages over tophat

[frymor]

Hi everybody,

I am working of RNA-Seq data and would like to map them using bowtie and/or tophat.

I know that tophat calls for bowtie first, but it is quite difficult to set certain parameters in tophat.
bowtie on itself is therefore a bit more forthcoming. Here I can set the parameters as I wish.

So my question is:

Does it make sense to run only tophat for the complete read file, or will it be better first to run bowtie with my own parameters and than only run tophat for the reads which weren't mapped in bowtie?

Do I waste my time on the second analysis, or is it the better way?

Thanks for help
Assa

[ffinkernagel]

Tophat does need the first stage genome alignment to define 'islands' of expression.
It should be possible to convince it to use your custom bowtie output though.

(You can also make yourself a local copy of tophat, and patch the parameters it passes to bowtie. Dirty, but quick).

[zee]

Take a look at RUM http://www.cbil.upenn.edu/RUM/userguide.php

RUM uses bowtie for optimal mapping of RNASeq alignments. In fact it would probably even be better to use have a version of RUM using a gapped aligner.

[kopi-o]

I thought RUM already uses BLAT for the gapped alignments.