Re: mg-rast Re: 454 - account already made for Bergen data
Folker, One more thing. The taxanomic heat map....how is it constructed, what taxanomic affiliation does it use to infer relative abundance, protein BLAST hits or some kind of phylogenetic marker? Cheers Jack On 9/17/07, Jack Gilbert <[email protected]> wrote:
Folker or Rob,
Is there any reason why I might get an incomplete blast search results page...it looks like when i search against our data it returns nothing....even for genes that SEED suggests are found in the data.
Link fault?
Let me know
jack
On 9/17/07, Jack Gilbert <[email protected]> wrote:
folker,
I agree with dawn, but would go further to suggest that a sequence identity matrix (% identity for each) for the 16S seqs from each pyroseq run would be a great, it would mean that we would not have to pull out individual 16S seqs and run this operation here.
Dawn,
You submitted 630 and 632 to the SEED it has been run with the new database, hence the 64% sequences found in the database.
I have uploaded the new seqs to SEED hopefully these will be done by tomorrow, if not by today.
re. clustering, lets talk about this tomorrow. It might give us something interesting and if there is a less labour intensive way of doing it then I would jump on it. However, it might not. There is no real link between what clustering tells us and the statistical analysis performed by Rob, which I was surprised about. anyway talk about this tomorrow.
There was a small prob with the pyro run from Liverpool and so we have got less than an anticipated but he is re running the samples and hopefully will get it sorted, so should end up with more than we requested. DNA will be done soon as well....this is essential for the comparison between GC-20 and Flx...that is supposed to be done by end of this week...fingers crossed.
I will have a word with Neil, but he is going away for a while, so will have to see how long it will take.
folker, thank you for your help, I am keen to see what would happen when silva is introduced....although the short seq reads might cause F-O and Wolfgang some consternation!
Cheers
Jack
On 9/17/07, Dawn Field <[email protected]> wrote:
Doh...forgot who I was talking to :-) Great if Silva can be grabbed - do you have a timeline?
Yes, it would be fabulous to meet up. You are more than welcome to visit Oxford. We can set you up a seminar or do something more casual - where will you be?
We should get initial feedback on the river microbe proposal next week and a more final decision next month - I think they will come back to PIs for more information - and knowing updates to the SEED will be really helpful.
I don't know if Rob had time to debrief you from the US-EU Task force but Stefan Schuster presented on MEGAN. I think he and Rob worked out a way to build a plugin to the SEED that would output data ready for viewing in MEGAN - just to confirm we'd be really keen on this.
Also really keen on having on diversity matrix ( samples in columns, taxa in rows, in a square matrix) produced from that taxonomy analysis but perhaps downstream after sliva (as we can manually make these here) and fasta files of just 16S (maybe this is already there, just haven't seen it).
Dawn
Folker Meyer <[email protected]> 9/17/07 14:28 >>> Dear Dawn,
I will send an email to Frank Oliver.
Cheers, Folker PS: I am planning to be in Europe some time in early November for a workshop. If there is any reason to meet that would be a good time.
On Sep 17, 2007, at 8:13 AM, Dawn Field wrote:
Dear Folker,
I don't know if Rob has already mentioned this but we would really love to have the Silva database behind SEED for the sake of making taxonomic assignments.
It is great, the largest 16S database around now, actively developed and has all three domains. Rob thought it was a good idea too :-)
If you don't already have connections, we can put you in touch with the developers if there are any issues to clarify before considering it.
I assume (?) it's as simple as downloading and putting another option in the pipeline?
Dawn
Folker Meyer < [email protected]> 9/17/07 12:21 >>> Jack:
so ensure compatibility we did run all old metagenomes against a stable version of our internal databases.
Now we updated all DBs used for analysis. The first runs were previously analyzed with a rather ancient version of our NR (non redundant protein database) and also a very old subsystem collection.
This explains the dramatic change. The current subsystem collection has more than 600 subsystems (old one had significantly less) and covers approx. 40-50% of all proteins in Strep., Staph, or Ecoli etc...
Hope that helps, Folker
On Sep 17, 2007, at 5:51 AM, Jack Gilbert wrote:
Rob and/or mg-rast techs.
just looking at the sequencing data from the first 454 runs (Bag1 and Bag6, 630 and 632) and the number of sequences that are found within subsystem catagories has leapt from 24% to 64%.....this seems amazing to me.
Does this mean that SEED has suddenly expanded to include a lot more information or is this due to a new analysis technique...interested to know.
Jack
On 9/14/07, Rob Edwards < [email protected]> wrote: Jack, Dawn,
I'm forwarding this to our internal mailing list for developers that work on the metagenomics RAST for two reasons - its great to see some praise once in a while in amongst all the people that get stuck or have problems, and also because they can answer all the specifics of what is being done and how.
Rob
Begin forwarded message:
From: "Jack Gilbert" < [email protected]> Date: September 14, 2007 4:51:31 AM PDT To: "Dawn Field" < [email protected]> Cc: [email protected] Subject: Re: 454 - account already made for Bergen data
Dawn and Rob,
I know I saw all the menus but from my end I can only see the diversity info for protein sequences not for rdp, green genes or ERD.
I agree the taxanomic comprison heatmap is fantastic. However, what is used to construct it?
Jack
On 9/14/07, Dawn Field <[email protected]> wrote: Hi Jack! The 16S is in there just like before - under the organism menu there is a way to look at taxonomy...You are right, looking at this first should really help. I have made rarefaction curves of the first two samples and compared overall diversity for just the bacteria and we can discuss the results. Past is really easy so we can do more with the new samples as well. If you can get out abundances
even just for RDP before Tuesday it would be great.
Rob - One nice output of the server is a column row file of diversity (a square matrix) ready for import into software like Past. I'll pass it on to Folker!
all the best, Dawn
-- Dr. Jack A. Gilbert B.Sc. Ph.D. Molecular Ecologist Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK. Work Tel: +44 (0)1752 633 416 Home Tel: +44 (0)1752 255 783 Mobile Tel: +44 (0)7764 190 147 Email: [email protected]
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-- Dr. Jack A. Gilbert B.Sc. Ph.D. Molecular Ecologist Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK. Work Tel: +44 (0)1752 633 416 Home Tel: +44 (0)1752 255 783 Mobile Tel: +44 (0)7764 190 147 Email: [email protected]
-- Dr. Jack A. Gilbert B.Sc. Ph.D. Molecular Ecologist Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK. Work Tel: +44 (0)1752 633 416 Home Tel: +44 (0)1752 255 783 Mobile Tel: +44 (0)7764 190 147 Email: [email protected]
-- Dr. Jack A. Gilbert B.Sc. Ph.D. Molecular Ecologist Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK. Work Tel: +44 (0)1752 633 416 Home Tel: +44 (0)1752 255 783 Mobile Tel: +44 (0)7764 190 147 Email: [email protected]
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Jack Gilbert