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

Re: [mg-rast] metagenome analysis/organism classification/barchart option does not work 06042011
by Mark D'Souza 28 Apr '11

28 Apr '11

Hi, This has now been fixed. Once again, thanks for bringing it to our attention. Regards, Mark On Apr 28, 2011, at 10:35 AM, Mark D'Souza wrote: > Hi, > > Thanks for letting us know about the problem, we are fixing it right now. > > Regards, > Mark > > > > On Apr 28, 2011, at 8:03 AM, Vladimir Sentchilo wrote: > >> Thank you for fixing bug [I had not checked it yet though] >> There is another problem with FIND option in the main menu [right upper corner] >> When pressing magnifying glass sign, an error message appears as below >> >> Can't call method "job_id" on an undefined value at /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_0_4/common/lib/MGRAST/Metadata.pm line 697. >> >> Is it something familiar to you? >> >> Best wishes >> Vladimir >> >> >> >> On 21/04/2011 22:03, Mark D'Souza wrote: >>> Hi, >>> >>> This problem was fixed with the last code update, thanks for reporting it. >>> >>> Regards, >>> Mark >>> >>> >>> >>> On Apr 6, 2011, at 11:03 AM, Mark D'Souza wrote: >>> >>> >>>> Hi, >>>> >>>> We are looking into this, thanks for letting us know about the problem. >>>> >>>> ----- Original Message ----- >>>> >>>>> From: "Vladimir Sentchilo"<vladimir.sentchilo(a)unil.ch> >>>>> To: mg-rast(a)mcs.anl.gov >>>>> Sent: Wednesday, April 6, 2011 8:51:49 AM >>>>> Subject: [mg-rast] metagenome analysis/organism classification/barchart option does not work 06042011 >>>>> Hello MGRAST team >>>>> Thank you for great server... >>>>> Today there are some problems with barchart drawing option. >>>>> In fact, chart has no bars and also clicking on classification >>>>> categories return false unfolding, for example click on Bacteria >>>>> returns >>>>> Archea group unfolded. >>>>> >>>>> Best regards >>>>> >>>> -- >>>> Regards, >>>> Mark D'Souza >>>> -- for the MG-RAST team >>>> >>>> mg-rast(a)mcs.anl.gov >>>> http://metagenomics.anl.gov/ >>>> >>>> If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov >>>> >>> >>> >

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Interpretation of Abundance Counts
by Jesse Port 28 Apr '11

28 Apr '11

Hi there, I had a question regarding your 'abundance count' metric. According to the analysis tools discussion it is defined as the number of times a particular taxon is detected. But I'm not exactly sure what that means, as the total abundance count for all taxonomic hits for a metagenome is much higher than the number of sequence reads. I'd just like to know the number of reads that were assigned to a given taxonomic group. Can the abundance count be thought of as a proxy for the read count assigned to a given taxonomy? If not how might one interpret this metric when comparing across different metagenomes? Thanks, Jesse

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Re: [mg-rast] regarding the MG-RAST already uploaded genomes
by Mark D'Souza 28 Apr '11

28 Apr '11

Dear Dr. Sena, It appears that I completely misunderstood your question and my previous response is inaccurate. The identifier (e.g. 4454195.3) assigned to your dataset by MG-RAST functions as the accession number and can be used to permanently link to this dataset. Once your dataset is made public this accession number can be used by anyone to view the MG-RAST analysis. We are adding a section to the MG-RAST blog at http://blog.metagenomics.anl.gov/howto/ which will explain in greater detail and will describe the formatting of the link you can enter in your publication. Regards, Mark On Apr 26, 2011, at 10:26 PM, suchitra sena wrote: > Dear Mark, > I have prepared a paper on taxonomic classification . I would like to know that how can I get the accession numbers. Whether each locus has to be submitted to ncbi genebank or any thing is there in MG-RAST software so that I can get accession numbers so that I can mention in publication. Whether all the locuses can be submitted for getting accession numbers at a time or to be submitted individually. How can I see or visualise the locus id and the respective sequences. > Regards > D. SuchitraSena > On Tue, Apr 26, 2011 at 10:32 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > Dear Dr. Sena, > > The two jobs you submitted to MG-RAST were completed on April 2nd and are available for viewing. If you log in to the MG-RAST version 3 site at http://metagenomics.anl.gov/metagenomics.cgi and click on the 'Browse' button in the top right hand corner and then you can view the list of your metagenomes by clicking on the number next to 'Available for analysis' as shown in the attached image. > > > > > We encourage you to make your data public through MG-RAST after publication, our policy regarding data retention is available at http://blog.metagenomics.anl.gov/mg-rast-v3-0-faq/#question8 > > Regards, > Mark D'Souza > -- for the MG-RAST team > > mg-rast(a)mcs.anl.gov > http://metagenomics.anl.gov/ > > If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov > > > > > On Apr 25, 2011, at 10:01 PM, suchitra sena wrote: > > > Sir, > > I have uploaded two metagenomes in the month of January 3rd week i.e., job No.'s assigned as 13802 and 13803. Now I am unable to see the data and these jobs are not there in my login account and I would like to know how I can get these data or kindly provide me this as I am in the process of data analysing and preparing for publications. Kindly also let me know that till how many days the data can be visualised further after sending. Submitted for an earlier reply in this regard. > > Thanking you, > > Yours faithfully, > > D. Suchitra Sena, > > Senior Scientist, > > >

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Fwd: Data analysis
by Mark D'Souza 28 Apr '11

28 Apr '11

Hi Tobi, Can you take a look into this? I confirmed that this bug exists, I clicked on Potassium Metabolism and the level 2 category displayed is Photosynthesis. Thanks, Mark Begin forwarded message: > From: Torey Looft <tlooft(a)iastate.edu> > Date: April 28, 2011 10:16:11 AM CDT > To: mg-rast(a)mcs.anl.gov > Subject: [mg-rast] Data analysis > > Hello, > > I think I have noticed a problem with the barchart section of your organism and functional classification analysis. When I use the p-value option, and I click on the categories (at each level distribution) the category that is expanded below isn't the one I clicked on. For example, if I click on nitrogen metabolism on level one, level two shows Clustering-based subsystem rather than the expanded nitrogen metabolism. I think I only noticed this with the p-vale option being used, but I what to use it for comparing groups. Thanks for your time! > > Best, > Torey

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Re: [mg-rast] Data analysis
by Mark D'Souza 28 Apr '11

28 Apr '11

Hi, Sorry about that, we will investigate and get it fixed, thanks for letting us know about the problem. Regards, Mark D'Souza -- for the MG-RAST team mg-rast(a)mcs.anl.gov http://metagenomics.anl.gov/ If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov On Apr 28, 2011, at 10:16 AM, Torey Looft wrote: > Hello, > > I think I have noticed a problem with the barchart section of your organism and functional classification analysis. When I use the p-value option, and I click on the categories (at each level distribution) the category that is expanded below isn't the one I clicked on. For example, if I click on nitrogen metabolism on level one, level two shows Clustering-based subsystem rather than the expanded nitrogen metabolism. I think I only noticed this with the p-vale option being used, but I what to use it for comparing groups. Thanks for your time! > > Best, > Torey

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Re: [mg-rast] metagenome analysis/organism classification/barchart option does not work 06042011
by Mark D'Souza 28 Apr '11

28 Apr '11

Hi, Thanks for letting us know about the problem, we are fixing it right now. Regards, Mark On Apr 28, 2011, at 8:03 AM, Vladimir Sentchilo wrote: > Thank you for fixing bug [I had not checked it yet though] > There is another problem with FIND option in the main menu [right upper corner] > When pressing magnifying glass sign, an error message appears as below > > Can't call method "job_id" on an undefined value at /mcs/bio/mg-rast/prod/FIGDisk/dist/releases/mgrast_release_3_0_4/common/lib/MGRAST/Metadata.pm line 697. > > Is it something familiar to you? > > Best wishes > Vladimir > > > > On 21/04/2011 22:03, Mark D'Souza wrote: >> Hi, >> >> This problem was fixed with the last code update, thanks for reporting it. >> >> Regards, >> Mark >> >> >> >> On Apr 6, 2011, at 11:03 AM, Mark D'Souza wrote: >> >> >>> Hi, >>> >>> We are looking into this, thanks for letting us know about the problem. >>> >>> ----- Original Message ----- >>> >>>> From: "Vladimir Sentchilo"<vladimir.sentchilo(a)unil.ch> >>>> To: mg-rast(a)mcs.anl.gov >>>> Sent: Wednesday, April 6, 2011 8:51:49 AM >>>> Subject: [mg-rast] metagenome analysis/organism classification/barchart option does not work 06042011 >>>> Hello MGRAST team >>>> Thank you for great server... >>>> Today there are some problems with barchart drawing option. >>>> In fact, chart has no bars and also clicking on classification >>>> categories return false unfolding, for example click on Bacteria >>>> returns >>>> Archea group unfolded. >>>> >>>> Best regards >>>> >>> -- >>> Regards, >>> Mark D'Souza >>> -- for the MG-RAST team >>> >>> mg-rast(a)mcs.anl.gov >>> http://metagenomics.anl.gov/ >>> >>> If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov >>> >> >>

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Data analysis
by Torey Looft 28 Apr '11

28 Apr '11

Hello, I think I have noticed a problem with the barchart section of your organism and functional classification analysis. When I use the p-value option, and I click on the categories (at each level distribution) the category that is expanded below isn't the one I clicked on. For example, if I click on nitrogen metabolism on level one, level two shows Clustering-based subsystem rather than the expanded nitrogen metabolism. I think I only noticed this with the p-vale option being used, but I what to use it for comparing groups. Thanks for your time! Best, Torey

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questions about MG-Rast analysis pipelines
by Alexandre Barretto de Menezes 28 Apr '11

28 Apr '11

Hi, I started to use MG-Rast recently and I have a few questions about some of its features. I would very grateful to any help in answering the following: 1. My samples are from environmental RNA, should I use sequence dereplication? Dereplication removed between around 23 to 37% of the quality checked sequences. 2. What alignment length and sequence identity cut offs were used to determine the number of rRNA sequences from each database in the hit source distribution? 3. I have doubts about the hit source distribution graph: a sequence may represent hits in different database sources (as in Genbank and TrEMBL)? Or once a best hit was found the respective sequence is removed from subsequent database searches? Thank you in advance Alex

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Re: [mg-rast] regarding the MG-RAST already uploaded genomes
by Mark D'Souza 27 Apr '11

27 Apr '11

Dr. Sena, This is not possible right now. A number of our users have told us that they would like access to information like this and we will try and make this available in the future. I am afraid this will not help you with the preparation of your paper right now. Regards, Mark On Apr 26, 2011, at 10:26 PM, suchitra sena wrote: > Dear Mark, > I have prepared a paper on taxonomic classification . I would like to know that how can I get the accession numbers. Whether each locus has to be submitted to ncbi genebank or any thing is there in MG-RAST software so that I can get accession numbers so that I can mention in publication. Whether all the locuses can be submitted for getting accession numbers at a time or to be submitted individually. How can I see or visualise the locus id and the respective sequences. > Regards > D. SuchitraSena > On Tue, Apr 26, 2011 at 10:32 PM, Mark D'Souza <dsouza(a)mcs.anl.gov> wrote: > Dear Dr. Sena, > > The two jobs you submitted to MG-RAST were completed on April 2nd and are available for viewing. If you log in to the MG-RAST version 3 site at http://metagenomics.anl.gov/metagenomics.cgi and click on the 'Browse' button in the top right hand corner and then you can view the list of your metagenomes by clicking on the number next to 'Available for analysis' as shown in the attached image. > > > > > We encourage you to make your data public through MG-RAST after publication, our policy regarding data retention is available at http://blog.metagenomics.anl.gov/mg-rast-v3-0-faq/#question8 > > Regards, > Mark D'Souza > -- for the MG-RAST team > > mg-rast(a)mcs.anl.gov > http://metagenomics.anl.gov/ > > If you need to respond to this email please address it to the mailing-list mg-rast(a)mcs.anl.gov > > > > > On Apr 25, 2011, at 10:01 PM, suchitra sena wrote: > > > Sir, > > I have uploaded two metagenomes in the month of January 3rd week i.e., job No.'s assigned as 13802 and 13803. Now I am unable to see the data and these jobs are not there in my login account and I would like to know how I can get these data or kindly provide me this as I am in the process of data analysing and preparing for publications. Kindly also let me know that till how many days the data can be visualised further after sending. Submitted for an earlier reply in this regard. > > Thanking you, > > Yours faithfully, > > D. Suchitra Sena, > > Senior Scientist, > > >

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Re: [mg-rast] Early access of NIH HMP oral metagenome data
by Mark D'Souza 27 Apr '11

27 Apr '11

Hi Felicia, You need to select a KEGG map as well as the genomes for comparison, send email to info(a)theseed.org if you continue to have problems using the seedviewer site. Regards, Mark On Apr 27, 2011, at 1:39 PM, Felicia Qi wrote: > Hi Mark, > > I found the kEGG comparison function in the SEED database, but it did not seem to be working - after I selected the genomes and clicked "select", nothing happened. > > I also tried to use the function-based comparison. The problem is, it always use the first genome on the list as reference, it would not allow me to compare 2 genomes as I chose. > > Is there a way to get either to work? Thanks. > > Felicia > On Apr 27, 2011, at 10:08 AM, Mark D'Souza wrote: > >> Felicia, >> >> The KeggMapper can be used for metagenomic samples only, the SeedViewer (http://seed-viewer.theseed.org/) has a similar KEGG comparison capability which =does= compare microbial species in the SEED database. >> >> Regards, >> Mark >> >> ----- Original Message ----- >>> From: "Felicia Qi" <Felicia-Qi(a)ouhsc.edu> >>> To: "Mark D'Souza" <dsouza(a)mcs.anl.gov> >>> Sent: Tuesday, April 26, 2011 7:29:50 PM >>> Subject: Re: [mg-rast] Early access of NIH HMP oral metagenome data >>> Hi Mark, >>> >>> I have another question. How to use Keggmapper to compare the genome >>> of two microbial species? Thanks. >>> >>> Felicia >>> On Apr 26, 2011, at 6:35 PM, Mark D'Souza wrote: >>> >>>> That is the problem, when you log in you should see a message: >>>> Warning: This application has been optimized for the Firefox >>>> browser. Since you are using Safari, some features may not be >>>> available. Firefox is freely available here ... >>>> >>>> you will need to get Firefox to use the KeggMapper. >>>> >>>> Regards, >>>> Mark >>>> >>>> >>>> >

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