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Forum: Metagenomics 11-06-2014, 12:22 AM
Replies: 13
Views: 4,602
Posted By overflow
supply metadata file and it will work, no idea...

supply metadata file and it will work, no idea why you have to do that...
Forum: Metagenomics 11-04-2014, 05:19 AM
Replies: 13
Views: 4,602
Posted By overflow
for PCA etc. you need to supply a metadata file,...

for PCA etc. you need to supply a metadata file, otherwise you will only be able to compare 2 samples
Forum: Metagenomics 11-04-2014, 04:09 AM
Replies: 13
Views: 4,602
Posted By overflow
just had the same problem, did you also include a...

just had the same problem, did you also include a metadata file?
Forum: Metagenomics 11-03-2014, 06:04 AM
Replies: 13
Views: 4,602
Posted By overflow
there is a conversion tool for mothur data...

there is a conversion tool for mothur data integrated (whatever that means because I'm not familiar with mothur).
However, at the end STAMP uses tables as input, so you should be able to import your...
Forum: Metagenomics 11-03-2014, 12:18 AM
Replies: 3
Views: 4,497
Posted By overflow
http://qiime.org/scripts/assign_taxonomy.html ...

http://qiime.org/scripts/assign_taxonomy.html
or even faster
http://qiime.org/scripts/parallel_assign_taxonomy_blast.html

use that + silva nr ssu.
however, you still have to separate sequences...
Forum: Metagenomics 11-03-2014, 12:10 AM
Replies: 13
Views: 4,602
Posted By overflow
Hi Richa, have you tried STAMP...

Hi Richa,

have you tried STAMP (http://kiwi.cs.dal.ca/Software/STAMP)? You could also use some of the QIIME scripts (http://qiime.org/tutorials/tutorial.html).

cheers!
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