June 2011 - Mg-rast - mailman3.cels.anl.gov

download
by Dongmei.Li＠csiro.au 01 Jun '11

01 Jun '11

Dear MG-RAST team, Thank you so much for your help. I have encounter another problem in download the data. In the attached fig. I tried to download in reads in "Function Distribution (Inorganic Sulfur Assimilation)" section (bottom line of Page 2), it did not work. It will be great if you can give me some advice on how to download it. Thank you in advance. Regards, Dongmei Dr. Dongmei Li Research Scientist| MEOR CSIRO Food & Nutritional Sciences Phone: +61 2 9490 5078 | Fax: +61 2 9490 5010 dongmei.li(a)csiro.au | www.csiro.au | www.csiro.au/CFNS Address: 11 Julius Ave. North Ryde,NSW 2113 PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.

1 0

Re: [mg-rast] A Question
by Andreas Wilke 31 May '11

31 May '11

no , we will put the download functionality in the overview page showing a diagram of all steps performed. On May 31, 2011, at 4:50 PM, Mark D'Souza wrote: > OK, Will just pointed me at the '&sims=1' trick to get the extended download page. Is this feature going to be released to our users in 3.1? > > Mark > > > On May 31, 2011, at 4:41 PM, Mark D'Souza wrote: > >> Hi Travis, (or anyone else familiar with this operation) >> >> Is it possible to get all read annotations for a job through the 3.1 workbench? >> >> Thanks, >> Mark >> >> >> >> On May 31, 2011, at 2:36 PM, Aaron Garoutte wrote: >> >>> Hello MG-RAST Team >>> >>> >>> I put some assemblies through your pipeline. Now that I have the contigs annotated I would like to go back and map my raw reads to the contigs to get a better measure of abundance. To do this I need to know how each contig has been annotated. I found (under metagenome downloads) the gene clustering file. This lists the contigs that cluster together and has, what I assume is a group name like aa90_105. So my question is, this there a file I can download that links the clustered contigs (via the cluster name) to the subsystem annotation? >>> >>> >>> As always thanks for your help >>> >>> >>> Aaron >>> >> > Andreas Wilke Argonne National Laboratory Mathematics and Computer Science Division Bldg. 240 , 4F8 9700 South Cass Avenue Argonne, IL 60439 (630) 252-3190 (phone) (630) 252-5986.(fax)

1 0

Dereplication error
by Gustavo B. Gregoracci 31 May '11

31 May '11

Hello there, I've submitted 7 metagenomes for processing earlier today and it seems there is a problem. When I checked the status a dereplication error is showing in each metagenome. Can I do something about it or is it a MG-Rast error? Can you check this for me? My username is montedeletras ... Thanks in advance for the help, Best regards, Gustavo Gustavo Bueno Gregoracci -- MSc., Dr. in Microbiology (Genetics and Molecular Biology) Email: gustavo_biomed(a)yahoo.com -- Pos doc Student Laboratório de Microbiologia (Prof. Fabiano Thompson) Centro de Ciências de Saúde - Instituto de Biologia - UFRJ Tel: +55 (21) 2562-6567

1 0