I've several questions regarding multiplex data and its analysis. 
First, I'm using a MiSeq run on 96-plex (dual index) data. While our current 
MiSeq data has had the machine the adapters ( including the indexes), it would 
be nice to be able to clip adapters using a file of adapters rather than one at 
a time for our older data, which didn't have the adapter clipped. 

Second, we have the MiSeq run a BWA alignment to the refererence genome for 
each (96) sample. The folder containing them all averages at about 5GB of data. 
I noticed that on a local version of Galaxy, a user with administrator 
privileges can load multiple files. But how can a regular user load them to the 
main galaxy? I've been reading the developer thread-is this something that will 
be released soon-ish? 

Third, Is there a way to run a workflow , several Samtools and Picard analysis, 
on multiple files so they all get processed? 


Ann Holtz-Morris, M.S. 
de Jong Laboratory 

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