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. 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? Thanks Ann -- Ann Holtz-Morris, M.S. SRA III de Jong Laboratory CHORI aholtzmorris@chori.org
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-gal...
Best! Jen Galaxy team
Thanks Ann
-- Ann Holtz-Morris, M.S. SRA III de Jong Laboratory CHORI aholtzmorris@chori.org
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-- Jennifer Hillman-Jackson http://galaxyproject.org
On 1/2/14 5:35 AM, Jennifer Jackson wrote:
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:
Hi Ann, I did miss pasting in the link to the ticket, thanks for pointing that out! Here it is: https://trello.com/c/CbFSHrU5 The Tool Shed is another place to follow along, in case a tool that meets your needs is created and shared there. I didn't see one yet, but new tools are added all the time. http://usegalaxy.org/toolshed Thanks! Jen Galaxy team
participants (2)
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Ann Holtz-Morris -
Jennifer Jackson