Forum: Metagenomics
10-07-2016, 04:56 AM
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Replies: 0
Views: 1,873
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...
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Forum: Metagenomics
02-09-2016, 09:27 AM
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Replies: 2
Views: 2,381
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Forum: Metagenomics
02-09-2016, 09:19 AM
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Replies: 3
Views: 3,128
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Forum: Metagenomics
02-09-2016, 06:42 AM
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Replies: 2
Views: 2,213
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Forum: Illumina/Solexa
12-15-2015, 12:22 PM
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Replies: 23
Views: 24,804
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...
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Forum: Bioinformatics
12-03-2015, 04:19 AM
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Replies: 2
Views: 3,033
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Forum: Metagenomics
12-02-2015, 11:20 AM
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Replies: 1
Views: 2,091
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Forum: Bioinformatics
11-24-2015, 10:49 AM
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Replies: 2
Views: 3,033
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Forum: Bioinformatics
10-27-2015, 08:56 AM
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Replies: 2
Views: 1,382
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.
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Forum: Bioinformatics
08-20-2015, 03:05 PM
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Replies: 7
Views: 2,405
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...
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Forum: Bioinformatics
06-02-2015, 11:30 AM
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Replies: 1
Views: 1,506
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,...
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Forum: Bioinformatics
06-02-2015, 11:13 AM
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Replies: 4
Views: 2,220
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...
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Forum: Bioinformatics
06-02-2015, 08:57 AM
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Replies: 1
Views: 1,476
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Forum: General
04-30-2015, 08:54 AM
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Replies: 7
Views: 2,101
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...
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Forum: Bioinformatics
04-30-2015, 08:28 AM
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Replies: 1
Views: 2,315
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...
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Forum: Bioinformatics
12-16-2014, 03:48 PM
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Replies: 1
Views: 1,617
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)...
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Forum: Metagenomics
07-15-2013, 08:16 AM
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Replies: 2
Views: 1,753
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Forum: General
02-22-2013, 07:43 AM
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Replies: 7
Views: 2,101
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Forum: General
02-22-2013, 07:02 AM
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Replies: 7
Views: 2,101
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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