On 12/20/13 3:43 PM, Ann Holtz-Morris wrote:
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
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?
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).
Ann Holtz-Morris, M.S.
de Jong Laboratory
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