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Old 04-07-2016, 04:00 AM   #1
ARSoares
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Location: Aberystwyth

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Lightbulb Using CLARK and EBI for metagenomes

Hello there,

Given Lindgreen et al. 2016 (http://www.nature.com/articles/srep19233), I am thinking of trying and use CLARK as a pre-processing/taxonomical analysis tool and the EBI webserver for functional analysis.

I am worried, however, that going from processing the raw files and analysis taxonomy with CLARK to functional analysis with EBI may cause problems.

Does CLARK output EBI-friendly files?

Anyone with background to give some input on this?

Thanks in advance.
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Old 04-07-2016, 07:48 AM   #2
fanli
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Are you talking about the EBI Metagenomics service? Seems like they want to start with raw fastq files (after human contaminant removal if applicable).
https://www.ebi.ac.uk/metagenomics/about

You might have to contact them about providing intermediate input. FWIW, here are a few lines of what the CLARK output looks like:
Quote:
TaxaName,Lineage,Count,Proportion_All(%),Proportion_Classified(%)
Acanthamoeba polyphaga mimivirus,;;;;Mimiviridae;Mimivirus,1,9.8806e-05,0.000131404
Acanthocystis turfacea Chlorella virus 1,;;;;Phycodnaviridae;Chlorovirus,1,9.8806e-05,0.000131404
Acetobacter pasteurianus,Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae;Acetobacter,4,0.000395224,0.000525615
Acetobacterium woodii,Bacteria;Firmicutes;Clostridia;Clostridiales;Eubacteriaceae;Acetobacterium,2,0.000197612,0.000262807
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Old 04-14-2016, 12:33 PM   #3
rouni001
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Dear all,

In the latest version (v1.2.3), the output (abundance) produced by CLARK rather looks like:

Name,TaxID,Lineage,Count,Proportion_All(%),Proportion_Classified(%)
Acanthamoeba polyphaga mimivirus,212035,;;;;Mimiviridae;Mimivirus,1,3.24058e-05,5.77055e-05
Acanthocystis turfacea Chlorella virus 1,322019,;;;;Phycodnaviridae;Chlorovirus,1,3.24058e-05,5.77055e-05
Acaryochloris marina,155978,Bacteria;Cyanobacteria;;Chroococcales;;Acaryochloris,9,0.000291652,0.00051935
Acetobacter pasteurianus,438,Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae;Acetobacter,8,0.000259246,0.000461644
Acetobacterium woodii,33952,Bacteria;Firmicutes;Clostridia;Clostridiales;Eubacteriaceae;Acetobacterium,22,0.000712927,0.00126952
...

The reported NCBI taxonomy id is what is needed to process organisms (with their read count) detected by CLARK.
If you have a specific need for your analysis then please feel free to post it in the forum of CLARK users:
https://groups.google.com/forum/#!forum/clarkusers

Best,
Rachid

Last edited by rouni001; 04-14-2016 at 01:46 PM.
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