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Forum: Metagenomics 10-07-2016, 03:56 AM
Replies: 0
Views: 1,738
Posted By fibar
EBI Metagenomics: How to analyze NCBI data?

Uploaded and public data from NCBI-SRA is mirrored and accessible at ENA (European Nucleotide Archive).
EBI Metagenomics (https://www.ebi.ac.uk/metagenomics) is a pipeline that analyzes data...
Forum: Metagenomics 02-09-2016, 08:27 AM
Replies: 2
Views: 2,271
Posted By fibar
Hi Mike, I'm interested in your post. As far as...

Hi Mike,
I'm interested in your post. As far as I know, what you say sounds good.
I haven't tried it yet, but maybe with anvi'o you can check where you are standing:...
Forum: Metagenomics 02-09-2016, 08:19 AM
Replies: 3
Views: 2,897
Posted By fibar
Hi, We've been using Velvet-MetaVelvet for a...

Hi,
We've been using Velvet-MetaVelvet for a same type of data set, and we are pretty happy with it.
Check steps at http://metavelvet.dna.bio.keio.ac.jp/
Cheers!
Forum: Metagenomics 02-09-2016, 05:42 AM
Replies: 2
Views: 1,931
Posted By fibar
MG-RAST - Alignment parameters of their process statistics?

After analyzing a metagenomic sample with MG-RAST, you go typically to the Metagenome Overview page to see how it performed.

At sections 'Metagenome Summary' and 'Analysis Flowchart' you have some...
Forum: Illumina/Solexa 12-15-2015, 11:22 AM
Replies: 23
Views: 24,407
Posted By fibar
Hi everyone, I go back to Pat Schloss:...

Hi everyone,
I go back to Pat Schloss: http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix%3F/
If you don't de-noise properly (ie. fully overlapped reads), you get too many unique...
Forum: Bioinformatics 12-03-2015, 03:19 AM
Replies: 2
Views: 2,901
Posted By fibar
Thanks GenoMax, that's what I was looking for.

Thanks GenoMax, that's what I was looking for.
Forum: Metagenomics 12-02-2015, 10:20 AM
Replies: 1
Views: 1,971
Posted By fibar
What's the best way to identify the taxonomy of assembled genomes?

Hi everyone,
Briefly, I applied coverage-based binning method plus pentamer-frequency ordination on metagenomic assembled contigs, to isolate individual genomes.

Now I'm looking for clever...
Forum: Bioinformatics 11-24-2015, 09:49 AM
Replies: 2
Views: 2,901
Posted By fibar
List of all sequenced Bacteria and their GC content

Hi everyone,
How is the best way to get a list of all names (full taxonomy if possible) of bacterial strains that were sequenced, plus their GC content (%).
e.g.
Proteobacteria Gammaprot....
Forum: Bioinformatics 10-27-2015, 07:56 AM
Replies: 2
Views: 1,302
Posted By fibar
Hi, Old thread, but I'm also interested in...

Hi,
Old thread, but I'm also interested in Olivia's topic.
This is typical for a metagenomic data set.
I did not see bacterial names at BioLists, suggested by Cedric.
Any other help?
Thanks.
Forum: Bioinformatics 08-20-2015, 02:05 PM
Replies: 7
Views: 2,250
Posted By fibar
I confirm GenoMax last reply. I updated my...

I confirm GenoMax last reply. I updated my version to 2.5.2 and it's working with the mentioned commands.

This new version includes the setting of a proxy at the 'vdb-config -i' window, which in...
Forum: Bioinformatics 06-02-2015, 10:30 AM
Replies: 1
Views: 1,428
Posted By fibar
MG-RAST - Efficient downloads?

Hello,
I want to download the hierarchical SEED Subsystems information for 30 metagenomes at MG-RAST. I've managed to obtain, through the API, the tables corresponding to the 4 levels separately,...
Forum: Bioinformatics 06-02-2015, 10:13 AM
Replies: 4
Views: 2,064
Posted By fibar
Hello, Good question, Soren. My suggestion...

Hello,
Good question, Soren.
My suggestion is to learn how to use the API, because one way to solve your problem is by downloading annotations directly. This is how I use it in the linux command...
Forum: Bioinformatics 06-02-2015, 07:57 AM
Replies: 1
Views: 1,303
Posted By fibar
It is more than just OK. But, as everything, it...

It is more than just OK.
But, as everything, it has pros and cons.
One of the major advantage is that you don't need local computational efforts, because everything is done at their servers.
And...
Forum: General 04-30-2015, 07:54 AM
Replies: 7
Views: 2,009
Posted By fibar
Thank you for your replies. What I meant...

Thank you for your replies.
What I meant originally was that NGS raw data should be made public whenever you publish the corresponding paper (which would contain the accession number). In my...
Forum: Bioinformatics 04-30-2015, 07:28 AM
Replies: 1
Views: 2,227
Posted By fibar
Hi, This is an old thread, but I'll answer...

Hi,
This is an old thread, but I'll answer anyway because I'm working on these things. In my opinion:
1st) It's recommended to upload fastq raw data to MG-RAST. That standarizes the procedure and...
Forum: Bioinformatics 12-16-2014, 02:48 PM
Replies: 1
Views: 1,485
Posted By fibar
Count BLAST hits and 'no hits'

I'm performing local blastn.
My query file consists in 20 sequences, and I have my own databases (DB) created out of several short reads Illumina files.

I ran the blastn (with e values > 1e-04)...
Forum: Metagenomics 07-15-2013, 07:16 AM
Replies: 2
Views: 1,684
Posted By fibar
Depth & Length for individual genome reconstructrion

Our goal: to reconstruct individual genomes from a metagenome
Our method: Illumina Hiseq paired-end sequencing

What would you choose between these 2 options?
- 150 bp long reads, with ~ 10Gbp...
Forum: General 02-22-2013, 06:43 AM
Replies: 7
Views: 2,009
Posted By fibar
Sorry, but what do you mean by "submitting their...

Sorry, but what do you mean by "submitting their data"?
Forum: General 02-22-2013, 06:02 AM
Replies: 7
Views: 2,009
Posted By fibar
Accession Numbers when publishing

Dear community, is it not obligatory to add an Accession Number whenever publishing results derived from NGS? I think it should be, I have found several articles with no numbers and that has stopped...
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