> My apologies if this has been covered before but I am using Galaxy Main and 
> wonder if, when running TopHat, you can modify the mapping parameters used by 
> Bowtie?

Not all Bowtie parameters can be modified when running Tophat. Which parameters 
are you looking to modify and why?

> It seems that the full parameter list for TopHat pertains only to the reads 
> that aren't mapped by Bowtie (the reads spanning splice junctions).

This should not be the case. For instance, documentation for the max-multihits 
discusses multiple hits when mapping reads junctions/segments:

If you're seeing different results, it may be a bug that could be discussed 
with the Tophat authors:

> Is there a way to access the full parameter list of Bowtie through TopHat?

Not currently.

> Or perhaps run Bowtie directly, then feed this into a TopHat run?

I don't think this is possible b/c Tophat uses the reads that map initially to 
build the coverage islands and then uses these islands to generate an index of 
potential splice junctions.


The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

Reply via email to