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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