[galaxy-user] Installing galaxy with Apache ...

Hi I've installed galaxy with the default settings and it works fine. On a new Ubuntu machine I am trying to get galaxy running with Apache. But I am having problems, I've followed the documentation. After installing Apache I can put my ip address into a browser and I get message saying Apac

Re: [galaxy-user] tophat deletions output

Hello Irene, The file is described in the TopHat manual: http://tophat.cbcb.umd.edu/manual.html#output Along with the insertion files, deletions describes variation between the query and the reference genome at the base level (nucleotide). It does not describe whole transcripts or genes. How

Re: [galaxy-user] inconsistent cuffdiff output

Hello Irene, It may be that the reference annotation GTF file was absent or did not have content for the transcript in the Cufflinks run that produced the "0" FPKM results. Then the reference annotation GTF used for Cuffdiff did. If the Cufflinks documentation about calculations does not alig

Re: [galaxy-user] How to find the alternatively spliced segment of genes in Cuffdiff output

Hello Jianguang, The file "Cuffdiff on data <...>: splicing differential expression testing" is described here: http://cufflinks.cbcb.umd.edu/manual.html#splicing_diff --> 5) Differential splicing tests - splicing.diff The CuffMerge file GTF output also has the TSSID attribute, in the 9th fie

Re: [galaxy-user] How to upload multiple files......

Hello Neil, This is correct - loading by file web browsing is one file at a time. And FTP is the usual solution, but there are other options. Multiple files from external sources can be loaded using the URL option. These would be http or ftp URLs. Multiple files from a local source (same co

[galaxy-user] Installing Galaxy and Hooking into a SGE Cluster

Hi guys, I want to install Galaxy on a local server and hook it into our SGE cluster. This excellent document seems to provide a lot of the steps http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster however I have two questions I'm not sure about. 1. Right now users keep their data in the

Re: [galaxy-user] New reference genome in Bowtie

Thanks Jen! That solved my problem. Sarah On 8/22/2012 10:59 AM, Jennifer Jackson wrote: Hello Sarah, We can add this genome to the list to be indexed for Bowtie. Meanwhile, quickest way to work with small genomes immediately is as a custom genome. Simply load the genome into your history in

Re: [galaxy-user] New reference genome in Bowtie

Hello Sarah, We can add this genome to the list to be indexed for Bowtie. Meanwhile, quickest way to work with small genomes immediately is as a custom genome. Simply load the genome into your history in fasta format and start using it with tools, including Bowtie. Just set these options to g

Re: [galaxy-user] file upload renamed

Hi Neil, You're looking for the option to "link to" data, which is explained here: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files --nate On Aug 22, 2012, at 12:44 AM, wrote: > When uploading a file using “Get Data” it seems the file is renamed to > dataset_’