Category Archives: Metagenomics Discussion Group

installing STAMP on a Mac

Since this was such a huge pain in the ass for so many of us, I figured I’d share what finally worked for me. First this: pip install STAMP then I got an error about matplotlib, so then this: pip … Continue reading

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Mendeley groups on environmental PCR, metagenomics, and microbial eukaryotes

As part of my NSF Research Coordination Network grant (RCN EukHiTS), I am currently managing a number of Mendeley groups that amalgamate relevant journal articles on different topics related to environmental PCR, metagenomics, and microbial eukaryotes. These groups are open … Continue reading

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Fryxell subsampled data and PhyloSift results

Jonathan has made available 50,000 reads from each of the Fryxell libraries here. Just in case you find this useful for testing. Also in this folder, there are PhyloSift results for each library (SampleAnt1-5).

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Annotation Databases

MG-RAST allows you to view the annotation of your data using several different annotation pipelines/databases. So, we had a discussion about them. Each database/tool was tackled by a different person: 1. GenBank/RefSeq – Joe 2. SEED/Subsystems – Jenna 3. COG/NOG/eggNOG … Continue reading

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Metagenomics Working Group – notes from 4/12/13

Guillaume ran us through the MG-RAST interface Question that came up again (to be asked at the QIIME workshop) – what is the difference between PCA and PCoA Canonical Correlation Analysis – a way to put vectors on your PCA … Continue reading

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Metagenomics Working Group

There are a number of people in and around the Eisen lab who are just starting to work with metagenomic (not 16S) data, and most (all?) of us have no idea what we’re doing! So, we’ve decided to meet weekly … Continue reading

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