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

Re: [mg-rast] HeatMap analysis?
by Mark DSouza 29 Aug '11

29 Aug '11

Hi, Thanks for the suggestions, I will add them as feature requests and we will consider making these changes. -- 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 ----- Original Message ----- > From: "Rick White" <raw937(a)gmail.com> > To: "Mark D'Souza" <dsouza(a)mcs.anl.gov>, mg-rast(a)mcs.anl.gov > Sent: Saturday, August 27, 2011 2:50:22 AM > Subject: Re: HeatMap analysis? > Hello again, > I also noticed that you can't export the rarefaction plot in a figure > format. > > It would be great to have this. > > Thank you > Rick > > > On Fri, Aug 26, 2011 at 3:41 PM, Rick White < raw937(a)gmail.com > > wrote: > > > > Hello Mark, > I have noticed that the scale bar isn't included with the image. > Also, the order of the samples doesn't in the order that you select. > > For example > I pick samples > A , B , C > > The analysis moves them all around in a different order. Would it be > possible to make the output in the order you select like the barchart? > > Thanks > Rick > > -- > > Richard Allen White III M.S. > PhD Student - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > V6T 1Z4 > ph. (604) 827-5715 > cell. ***My new number is 604-440-5150 *** > http://www.ocgy.ubc.ca/~suttle/ > > For Shipping: > Richard Allen White III & Amy Chan > Suttle Lab > UBC-Botany/zoology/micro > 1316-6270 University Blvd. > Vancouver, BC > V6T 1Z4 > 1.604.827.5715 > > > > > -- > > Richard Allen White III M.S. > PhD Student - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > V6T 1Z4 > ph.(604) 827-5715 > cell. ***My new number is 604-440-5150 *** > http://www.ocgy.ubc.ca/~suttle/ > > For Shipping: > Richard Allen White III & Amy Chan > Suttle Lab > UBC-Botany/zoology/micro > 1316-6270 University Blvd. > Vancouver, BC > V6T 1Z4 > 1.604.827.5715

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Re: [mg-rast] Something odd ID4451990
by Mark DSouza 29 Aug '11

29 Aug '11

Hi, We will look into this and get back to you when we have some more information. -- 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 ----- Original Message ----- > From: "Thomas Haverkamp" <t.h.a.haverkamp(a)bio.uio.no> > To: "MG- Rast" <mg-rast(a)mcs.anl.gov> > Sent: Saturday, August 27, 2011 8:23:26 AM > Subject: [mg-rast] Something odd ID4451990 > Hi, > While playing with the data of the metagenomes I uploaded to MG-RAST I > noticed something odd with one of the metagenomes. the MG-RAST ID is: > 4451990.3 (4T1a) > The thing I see in the overview table is this: > - Post QC: Sequences Count 1,155,434 ( nothing strange here) > > the odd thing comes in the Rank abundance plot: > the counts for proteobacteria: 2,241,332 > > This later value should not be possible if I have only 1.1 milion > reads. So I think something went wrong with this dataset. Could you > let me know what that exactly is and if you can rerun the annotation > of the dataset? My other datasets I checked and these seem to be okay. > there the numbers make sense and correspond to values I generated > myself using my own pipeline. > Cheers > Thomas > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > - - - - - - - - > Dr. Thomas H.A. Haverkamp > Centre for Ecological and Evolutionary Synthesis (CEES) > Dept. of Biology > University of Oslo > P.O. Box 1066 Blindern > 0316 Oslo Norway > > Phone: +47 22 85 45 23 > Mobile: +47 48 09 49 32 > E-mail: thhaverk(a)bio.uio.no > Skype: Thomieh73

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Fwd: Change of user name
by Mark DSouza 29 Aug '11

29 Aug '11

forward ----- Forwarded Message ----- > From: "Morten Poulsen" <Morten.Poulsen(a)agrsci.dk> > To: "Mark DSouza" <dsouza(a)mcs.anl.gov> > Sent: Monday, August 29, 2011 9:01:22 AM > Subject: Re: [mg-rast] Change of user name > Great! > > Thanks, > Morten > > > Den 29/08/2011 kl. 15.55 skrev Mark DSouza: > > Hi, > > I made the change, let us know if you have any problems logging in. > > -- > Regards, > Mark D'Souza > -- for the MG-RAST team > > mg-rast(a)mcs.anl.gov<mailto:[email protected]> > 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<mailto:[email protected]> > > > > ----- Original Message ----- > From: "Morten Poulsen" > <Morten.Poulsen(a)agrsci.dk<mailto:[email protected]>> > To: mg-rast(a)mcs.anl.gov<mailto:[email protected]> > Sent: Monday, August 29, 2011 8:30:50 AM > Subject: [mg-rast] Change of user name > How can I change my username (or alternatively delete my account and > create a new)? > > Old username: zP46JYgb > Wanted new username: Morten_Poulsen > > Cheers and thanks, > Morten > > _____ > > Med venlig hilsen / Regards > Morten Poulsen > Ph.d.-stipendiat / Ph.D. Fellow > > Section for Immunology and Microbiology > Dept. of Animal Health and Bioscience > Faculty of Science and Technology, Aarhus University > Blichers allé 20, P.O. BOX 50, DK-8830 Tjele > Direct: +45 89991160 > Mobile: +45 25150255 > E-mail: Morten.Poulsen(a)agrsci.dk<mailto:[email protected]> > _____ > > > _____ > > Med venlig hilsen / Regards > Morten Poulsen > Ph.d.-stipendiat / Ph.D. Fellow > > Section for Immunology and Microbiology > Dept. of Animal Health and Bioscience > Faculty of Science and Technology, Aarhus University > Blichers allé 20, P.O. BOX 50, DK-8830 Tjele > Direct: +45 89991160 > Mobile: +45 25150255 > E-mail: Morten.Poulsen(a)agrsci.dk<mailto:[email protected]> > _____

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Re: [mg-rast] Mapping to a model organism
by Mark DSouza 29 Aug '11

29 Aug '11

Hi, Can you tell us the MG-RAST metagenome ID for the dataset with this problem, and if you have the sequence IDs which should have been screened that would be very helpful, we will have to investigate and figure out what happened. -- 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 ----- Original Message ----- > From: "Jim Wallace" <jwallace(a)u.washington.edu> > To: mg-rast(a)mcs.anl.gov > Sent: Sunday, August 28, 2011 8:16:51 PM > Subject: [mg-rast] Mapping to a model organism > Hello, > > I'm seeing sequences screened against a model organism included in the > "other" category and subsequently matching the species of the model > organism in the analysis section. Are these sequences not matching > exactly using BowTie? > > Thanks, > > Jim > > -- > Jim Wallace > University of Washington > Institute for Risk Analysis and Risk Communication > Department of Environmental and Occupational Health Sciences > (206) 616-4876

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Re: [mg-rast] Change of user name
by Mark DSouza 29 Aug '11

29 Aug '11

Hi, I made the change, let us know if you have any problems logging in. -- 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 ----- Original Message ----- > From: "Morten Poulsen" <Morten.Poulsen(a)agrsci.dk> > To: mg-rast(a)mcs.anl.gov > Sent: Monday, August 29, 2011 8:30:50 AM > Subject: [mg-rast] Change of user name > How can I change my username (or alternatively delete my account and > create a new)? > > Old username: zP46JYgb > Wanted new username: Morten_Poulsen > > Cheers and thanks, > Morten > > _____ > > Med venlig hilsen / Regards > Morten Poulsen > Ph.d.-stipendiat / Ph.D. Fellow > > Section for Immunology and Microbiology > Dept. of Animal Health and Bioscience > Faculty of Science and Technology, Aarhus University > Blichers allé 20, P.O. BOX 50, DK-8830 Tjele > Direct: +45 89991160 > Mobile: +45 25150255 > E-mail: Morten.Poulsen(a)agrsci.dk<mailto:[email protected]> > _____

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Change of user name
by Morten Poulsen 29 Aug '11

29 Aug '11

How can I change my username (or alternatively delete my account and create a new)? Old username: zP46JYgb Wanted new username: Morten_Poulsen Cheers and thanks, Morten _____ Med venlig hilsen / Regards Morten Poulsen Ph.d.-stipendiat / Ph.D. Fellow Section for Immunology and Microbiology Dept. of Animal Health and Bioscience Faculty of Science and Technology, Aarhus University Blichers allé 20, P.O. BOX 50, DK-8830 Tjele Direct: +45 89991160 Mobile: +45 25150255 E-mail: Morten.Poulsen(a)agrsci.dk<mailto:[email protected]> _____

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Mapping to a model organism
by Jim Wallace 28 Aug '11

28 Aug '11

Hello, I'm seeing sequences screened against a model organism included in the "other" category and subsequently matching the species of the model organism in the analysis section. Are these sequences not matching exactly using BowTie? Thanks, Jim -- Jim Wallace University of Washington Institute for Risk Analysis and Risk Communication Department of Environmental and Occupational Health Sciences (206) 616-4876

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Re: [mg-rast] Something odd ID4451990
by William Trimble 27 Aug '11

27 Aug '11

Job 11679 The reads are medium-length, avg 350bp. There are 1.2M reads and 1.2 M features. So it isn't the gene calling step. There are only 14000 clusters, most have only two proteins, and none are large. It doesn't look like the clustering step, unless something is wrong. There are 450,000 features with similarities, so the hits -> abundance ratio is close to 4. Is this reasonable behavior from the annotation step? w On Sat, Aug 27, 2011 at 8:23 AM, Thomas Haverkamp <t.h.a.haverkamp(a)bio.uio.no> wrote: > Hi, > While playing with the data of the metagenomes I uploaded to MG-RAST I > noticed something odd with one of the metagenomes. the MG-RAST ID is: > 4451990.3 (4T1a) > The thing I see in the overview table is this: > - Post QC: Sequences Count 1,155,434 ( nothing strange here) > > the odd thing comes in the Rank abundance plot: > the counts for proteobacteria: 2,241,332 > > This later value should not be possible if I have only 1.1 milion reads. So > I think something went wrong with this dataset. Could you let me know what > that exactly is and if you can rerun the annotation of the dataset? My other > datasets I checked and these seem to be okay. there the numbers make sense > and correspond to values I generated myself using my own pipeline. > Cheers > Thomas > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > - - - - - > Dr. Thomas H.A. Haverkamp > Centre for Ecological and Evolutionary Synthesis (CEES) > Dept. of Biology > University of Oslo > P.O. Box 1066 Blindern > 0316 Oslo Norway > > Phone: +47 22 85 45 23 > Mobile: +47 48 09 49 32 > E-mail: thhaverk(a)bio.uio.no > Skype: Thomieh73 > >

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Something odd ID4451990
by Thomas Haverkamp 27 Aug '11

27 Aug '11

Hi, While playing with the data of the metagenomes I uploaded to MG-RAST I noticed something odd with one of the metagenomes. the MG-RAST ID is: 4451990.3 (4T1a) The thing I see in the overview table is this: - Post QC: Sequences Count *1,155,434* ( nothing strange here) the odd thing comes in the Rank abundance plot: the counts for proteobacteria: *2,241,332* This later value should not be possible if I have only 1.1 milion reads. So I think something went wrong with this dataset. Could you let me know what that exactly is and if you can rerun the annotation of the dataset? My other datasets I checked and these seem to be okay. there the numbers make sense and correspond to values I generated myself using my own pipeline. Cheers Thomas - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Dr. Thomas H.A. Haverkamp Centre for Ecological and Evolutionary Synthesis (CEES) Dept. of Biology University of Oslo P.O. Box 1066 Blindern 0316 Oslo Norway Phone: +47 22 85 45 23 Mobile: +47 48 09 49 32 E-mail: thhaverk(a)bio.uio.no Skype: Thomieh73

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Re: [mg-rast] HeatMap analysis?
by Rick White 27 Aug '11

27 Aug '11

Hello again, I also noticed that you can't export the rarefaction plot in a figure format. It would be great to have this. Thank you Rick On Fri, Aug 26, 2011 at 3:41 PM, Rick White <raw937(a)gmail.com> wrote: > Hello Mark, > I have noticed that the scale bar isn't included with the image. > Also, the order of the samples doesn't in the order that you select. > > For example > I pick samples > A , B , C > > The analysis moves them all around in a different order. Would it be > possible to make the output in the order you select like the barchart? > > Thanks > Rick > > -- > Richard Allen White III M.S. > PhD Student - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > V6T 1Z4 > ph.(604) 827-5715 > cell. ***My new number is 604-440-5150*** > http://www.ocgy.ubc.ca/~suttle/ > > For Shipping: > Richard Allen White III & Amy Chan > Suttle Lab > UBC-Botany/zoology/micro > 1316-6270 University Blvd. > Vancouver, BC > V6T 1Z4 > 1.604.827.5715 > > -- Richard Allen White III M.S. PhD Student - Suttle Lab Department of Microbiology & Immunology The University of British Columbia Vancouver, BC, Canada V6T 1Z4 ph.(604) 827-5715 cell. ***My new number is 604-440-5150*** http://www.ocgy.ubc.ca/~suttle/ For Shipping: Richard Allen White III & Amy Chan Suttle Lab UBC-Botany/zoology/micro 1316-6270 University Blvd. Vancouver, BC V6T 1Z4 1.604.827.5715

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