Hello,
How should I proceed with my raw functional gene sequencing data obtained from Roche 454.Which pipeline should I use to process the sequences?Which database should I use?
Any help on this matter will be highly appreciated.
Thanks..
Can you tell us, what you are trying to investigate? E.g.: phylogenetics, biogeography, functional protein analysis, ...
In addition it might be helpful to know what organisms the sequences where obtained from.
In general; when you ask questions here, try to provide as much information as possible. Keep in mind, that we do not know your project, your backgroud and your aims.
Cheers
Claudia
Hi,Thanks.
My study is focused on 'Studying the Changes in community structure of Nitrifying bacterial and archaeal community under different fertilization strategies and its correlation to soil parameters.'On that note,I sampled soils (each three replicates) receiving 5 different treatments [No Treatment(NT),Chemical Fertilizer(CF),Compost(CO),Chem. Fertilizer and Compost(FCO) and N-free(NFR)] from long term fertilized paddy fields.In total I have 15 samples.I isolated total soil DNA from each sample and performed Roche 454 sequencing of amoA gene of Bacteria and Archaea with specific primers.IMy objective is to check the changes in nitrfying community structure and its correlation to soil chemical parameters and productivity.
On that note how should I proceed.
Thanks,
Sandipan
Hi!
You can use QIIME pipeline (http://qiime.org/) for 16S sequences, but in the "Otu picking" step you need to change the parameters by default and use a database of amoA gene. After that you should have the OTU table (abundance of each OTU on each sample) and the corresponding taxonomical tables, and you can analyse them with some statistical software, like STAMP (http://kiwi.cs.dal.ca/Software/STAMP) .
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