Re: [galaxy-user] SAM to BAM conversion problem

2011-04-18 Thread Kelly Vincent
Hemant, This is really odd, and definitely not what should be happening. Would you mind sharing your history with me so I can take a closer look? While I'm looking into it, you should be able to manually change the database to ce6 and then run SAM-to-BAM. We have everything needed for

[galaxy-user] Map with Bowtie

2011-04-18 Thread Sher, Falak
Hi Colleagues, I mapped illumina sequences using Bowtie on Galaxy server, I could not locate the information, like how many there were total reads and in what percentage they are mapped with mouse genome etc (samples were from mouse). Help and suggestions are greatly acknowledged, Thank you

Re: [galaxy-user] [Gmod-help] Missing tools in my configured galaxy

2011-04-18 Thread Scott Cain
Hi Peter, I can't help you with that, so I'm going to forward this to the galaxy-user mailing list, galaxy-user@lists.bx.psu.edu, where presumably someone will know the answer. Scott On Mon, Apr 18, 2011 at 10:21 AM, Peter Tonge peter_ton...@hotmail.com wrote: Hi, I have configured Galaxy on

Re: [galaxy-user] [Gmod-help] Missing tools in my configured galaxy

2011-04-18 Thread Ross
To unpack this mystery, you need to follow the chain from tool_conf.xml (that's what the tool menu is made from) to the actual tool directory and xml file name - eg: rerla@rosst61:~/rgalaxy$ grep -i group tool_conf.xml .. tool file=stats/grouping.xml / .. That means you need to look in

Re: [galaxy-user] Map with Bowtie

2011-04-18 Thread Jennifer Jackson
Hello Falak, The tools in Text Manipulation, Filter and Sort, and Join, Subtract and Group are designed to help with this type of file analysis (basic stats). Please explore and let us know if you need help with any particular tool, Best, Jen Galaxy team On 4/18/11 7:47 AM, Sher, Falak

Re: [galaxy-user] database on the cloud

2011-04-18 Thread Enis Afgan
Hi Thomas, It turns out you discovered a bug in the cloud setup. We're missing a 2bit file and a respective reference to the file for the extract genomic DNA tool. We'll update the deployment but in the mean time you can configure the instance yourself with just a few commands: # connect to the

Re: [galaxy-user] database on the cloud

2011-04-18 Thread Blake L. Dixon
Take me off this list, please. - Original Message - From: Enis Afgan afg...@gmail.com Date: Monday, April 18, 2011 1:41 pm Subject: Re: [galaxy-user] database on the cloud To: Randall, Thomas (NIH/NIEHS) [C] thomas.rand...@nih.gov Cc: galaxy-user@lists.bx.psu.edu

Re: [galaxy-user] Map with Bowtie

2011-04-18 Thread Jennifer Jackson
Hello Falak, There may be another issue regarding metadata display we would like to confirm. Would you have time to share a link to your history? Options - Share or Publish. You can send the link directly to me. Please note which dataset is the Bowtie result in question, if there are multiple

Re: [galaxy-user] how to generate consensus sequence in galaxy

2011-04-18 Thread Jennifer Jackson
Hello Vaibhav, Genome assembly tools are available in the Galaxy Community Tool Shed. http://community.g2.bx.psu.edu/ Look under Browse by category - Assembly. Tools are donated by our user community and are designed to work on local installs.

Re: [galaxy-user] downstream analysis of cuffdiff out put

2011-04-18 Thread Jeremy Goecks
Vasu, Please reply to the mailing list as emails to individual Galaxy developers often get lost, and there are others on the list that might be able to help you or benefit from this discussion. Now, to your question: you're using the wrong GFF filtering tool, which is an easy mistake to