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Old 10-20-2010, 10:11 AM   #1
ssharma
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Default Illumina Metagenomics data

Hi All,
I am new member to this forum.
Earlier i used to work with 454 data, now i am switching to illumina.
I am getting around 300 million reads (100bp) and its a metagenomic sample. So i am really confused about how to start my analysis.
Earlier i used approaches like blastx but now i think this is not a good option.
So i was just wondering if anyone had done something like this or have some idea on this.

I would really appreciate your help.

Thanks
SS
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Old 10-21-2010, 12:24 AM   #2
rwenang
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Is it a 16S or WGS sample?
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Old 10-21-2010, 05:32 AM   #3
ssharma
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Its a metagenomics environmental sample (no 16s).
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Old 10-21-2010, 07:11 AM   #4
themerlin
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The real question is....what's the question? Are you looking for specific genes, or want to take an inventory of all genes?

Have you tried assembling the reads yet? That's always a little sketchy with mixed communities, but it might be a good place to start.
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Old 10-21-2010, 07:45 AM   #5
ssharma
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thanks for your input themerlin,
Actually mainly its going to be a community study (in nut shell i need to annotate all of the sequences)
Yes i tried assembly but it doesn't look good, but yes i will try again with different programs.
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Old 12-01-2010, 11:36 AM   #6
kmewis
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Is this just sequence data from DNA straight from the environment, or did you clone it into vectors first?

I handle metagenomics data, we do it in fosmids though, so it's easy to assemble contigs from one fosmid (phred/phrap). Trying to do the whole environment at once will likely be tougher. Once I have contigs, we use blastx to looks for homology and tools like fgenesb to find ORFs.
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Old 12-02-2010, 01:42 AM   #7
Dilipmohana
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hi i am new to this site can anyone tell me about effective working in schrodinger plz pass useful video tutorials if possible,
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Old 12-05-2010, 11:35 AM   #8
greigite
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Take a look at MG-RAST for annotation of your data http://metagenomics.nmpdr.org.
Quote:
Originally Posted by ssharma View Post
Hi All,
I am new member to this forum.
Earlier i used to work with 454 data, now i am switching to illumina.
I am getting around 300 million reads (100bp) and its a metagenomic sample. So i am really confused about how to start my analysis.
Earlier i used approaches like blastx but now i think this is not a good option.
So i was just wondering if anyone had done something like this or have some idea on this.

I would really appreciate your help.

Thanks
SS
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Old 12-10-2010, 08:00 AM   #9
Eric
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Hi,

What do you mean by "annotate" ? Are you looking at "who is there" or "what are the functions" ?
Do you have reference genomes at hand, or genomes of organisms close to the ones in your sample ? Do you have an idea of the complexity of the population ? Is it eukaryote or microbes, or both ?
You can consider first trying to have an idea of the composition of your population, looking at some marker genes (eg : trying to find 16S or 18S reads in your dataset by mapping against reference databases)
If you have known reference genomes, you can also map reads against them, to evaluate the complexity/diversity
For a first glimpse at functions, you can try UniRef50 or KEGG genes (or any other functionally classified reference protein set) as a proxy.
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Old 12-21-2011, 09:22 AM   #10
gridbird
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You can try WebMGA: http://weizhong-lab.ucsd.edu/metagenomic-analysis/
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Old 03-30-2012, 05:03 AM   #11
colindaven
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You can try approaches like
-de novo assembly (metaVelvet, Abyss etc)
-fast clustering - (CD-Hit, RAMMCAP)
-reference based alignment (Genometa)
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Old 04-04-2012, 09:09 PM   #12
faozhi
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I would trim the reads (based on qual and remove adapters), then start assembling.
If you would like to know who are there, you could use MG-RAST or just blastn your trimmed reads against greengenes or SILVA 16S databases.
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Old 04-05-2012, 11:55 AM   #13
seb567
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Quote:
Originally Posted by ssharma View Post
Hi All,
I am new member to this forum.
Earlier i used to work with 454 data, now i am switching to illumina.
I am getting around 300 million reads (100bp) and its a metagenomic sample. So i am really confused about how to start my analysis.
Earlier i used approaches like blastx but now i think this is not a good option.
So i was just wondering if anyone had done something like this or have some idea on this.

I would really appreciate your help.

Thanks
SS

You can reduce the volume of data by doing a de novo assembly.




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mpiexec -n 64 Ray \
 -k \
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 -o \
 Assembly

Sébastien Boisvert
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