User: lotus28

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lotus2860
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Posts by lotus28

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Functional Metagenomic Analysis Tools
... I am going to perform functional analysis on a large collection of WGS gut metagenomes. However, options are too numerous. There is MEGAN6, MOCAT2, others. For me resource efficiency is key. I have discovered [SUPER-FOCUS][1], that is claimed to be super-fast, but the lack of updates keeps me worrie ...
microbiome metagenomics protein function written 9 days ago by lotus2860
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Comment: C: Metagenomics best reference DB
... That's great news I am not sure that it counts as behind schedule. The announcement is from April 2018 and says that from Fall 2018 onwards SILVA will be free for all purposes. So, I believe that Silva is now free for commercial use. ...
written 9 weeks ago by lotus2860
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Comment: C: Metagenomics best reference DB
... That's interesting. Are you aware of any qiime2 compatible classifiers for RDP? ...
written 9 weeks ago by lotus2860
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Comment: C: Metagenomics best reference DB
... But RDP does not report taxa names below genus, does it? That is what I'd like the most from a ref DB, as I intend to use 16S as a "crutch" for my WGS study. ...
written 9 weeks ago by lotus2860
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Metagenomics best reference DB
... I cannot decide which reference I should use to map my gut microbiome 16S data. Greengenes seems to be the best choice, but last time it was updated in 2013 and metagenomics has moved far ahead since then. Won't I be missing a huge part of biodiversity, if I use it? Also, this [article][1] keeps me ...
greengenes metagenomics silva 16s written 9 weeks ago by lotus2860
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Gut microbe annotation DB
... As a result of my study I have received a number of bacterial species that are important for developing a medical condition. Now I would like to know, what are these bacteria's role in gut microbiome. I want to see which of them have invasive potential, what metabolites they feed on and what they p ...
gut microbiome bacteria ecology microbiology written 5 months ago by lotus2860 • updated 4 months ago by Dattatray Mongad260
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QIIME OTU-picking: doubles counts or not?
... I used QIIME's `pick_closed_reference_otus.py` with the latest greengenes dataset. But I couldn't find any info on how it treats reads that can be assigned both to a species and to a genus. Does it count this read twice: adding it both to genus and to species? Or just once: adding it only to the sp ...
otu-picking metagenome mapping qiime written 2.2 years ago by lotus2860
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Comment: C: QIIME: OTU-picking works way too long
... Logs stop at the point when I press enter. ...
written 2.3 years ago by lotus2860
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QIIME: OTU-picking works way too long
... I am trying to use [pick_closed_reference_otus][1] QIIME script to assign taxonomy to single-direction [16S RNA-reads][2]. To do so, I downloaded the latest [13_8 Greengenes DB][3]. I decided to test it with a small datasset in Virtual Box QIIME: pick_closed_reference_otus.py -i /media/sf_ena ...
otu 16s qiime written 2.3 years ago by lotus2860
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Comment: C: Comparison of 16S- & WGS-derived community composition
... Thank you for the reply, I'll be waiting for you. BTW, right now I'm trying to find compatible human gut metagenome data sets to study Crohn's disease (CD). So far, the HMP data looks big and good. It has 16S-metagenomes made with v1-v3, v3-v5 and v6-v9 primers and WGS-metagenomes. But CD-associate ...
written 2.3 years ago by lotus2860

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