Hello Ann,

On 12/20/13 3:43 PM, Ann Holtz-Morris wrote:

Hi,

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.

There are a few open enhancement request tickets related to adapter clipping in Trello. If you would like to follow along or add in comments, this is the primary ticket:

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?

An updated upload tool is in development. Meanwhile, FTP would be the best way to load multiple files.

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

Yes, at the time a workflow is executed, multiple inputs can be selected. This prior thread has a nice graphic in the first reply from Dannon (plus other details, e.g. pointers to the API if you are interested).
http://dev.list.galaxyproject.org/Looking-for-recommendations-How-to-run-galaxy-workflows-in-batch-td4362836.html

Best!

Jen
Galaxy team

Thanks

Ann

Ann Holtz-Morris, M.S.
SRA III
de Jong Laboratory
CHORI
aholtzmorris@chori.org

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