[galaxy-user] (no subject)

I have been unable to upload data files into Galaxy Main since Friday 18th May 2012. Today is my fourth day of attempting uploads. Refreshing and leaving the files to upload overnight does not work. Although Jennifer has stated the bug has been fixed at 5.30pm today I am still unable to upload d

Re: [galaxy-user] (no subject)

Hello Megan, Are you still experiencing problems now? Galaxy may have been busy immediately following the resolution of the cluster problem, although your problem does appear to be unrelated. It sounds like you are uploading file through a browser. A better choice would be to use FTP. This i

Re: [galaxy-user] Mapping paired end reads with Tophat

Hi Jiwen, The short answer is that if your data is not pairing, then there may be a quality problem. Or, there may be a problem with the TopHat mapping run. The best advice is to take a sample of your data and experiment with some TopHat alternate parameters (using the protocol suggestions in

Re: [galaxy-user] Maq consensus calling changes quality score of the read?

Hi Antony, Sorry for the delayed reply. Are you still having problems with Pileup? This isn't correct behavior - quality scores should be unchanged, which means they are most likely Phred33+. Can you reproduce this on the public main Galaxy instance now (Samtools has been updated since your