User: fyfes

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fyfes30
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Posts by fyfes

<prev • 27 results • page 1 of 3 • next >
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Comment: C: export edgeR normalised OTU table
... thank you, so it does normalise my data without doing cpm? ...
written 28 days ago by fyfes30
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export edgeR normalised OTU table
... Hello, I want to normalise my microbiome data (OTU table) using edgeR package and export my normalised matrix ( I want to test some normalisation methods, normalised data will serve to calculate beta diversity and visualise by PCoA). I went through bioconductor forum and biostars and I still don't ...
microbiome normalisation written 28 days ago by fyfes30 • updated 28 days ago by ATpoint46k
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export ANCOM-BC normalisation matrix
... Hello, I want to normalise my microbiome data (otu table) using ancom-bc (I want to have a csv file with data that is normalised for library size). I am doing that: feature.table=feature_table; sample.var="sample_id"; group.var="group" zero.cut=0.90; lib.cut=1000; neg.lb=FALSE pre.process=fea ...
microbiome normalisation written 28 days ago by fyfes30
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importing data from qiita to qiime artifact
... Hi, I have to process data from this qiita project: https://qiita.ucsd.edu/study/description/11052#. As no raw data in available I have downloaded preprocessed.fastq.gz from the demultiplexing triangle. However I am struggling since 3 days how to put it into a qiime artefact. As far as I know fastq ...
qiita sequencing written 3 months ago by fyfes30
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Comment: C: do we clone sequences while performing shotgun sequencing on microbiome?
... Hi, thank you so much Antonio. And the article is just yum :) ...
written 5 months ago by fyfes30
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do we clone sequences while performing shotgun sequencing on microbiome?
... Hi, I am reading about shotgun sequencing and I see that often it is written that: In shotgun method, the DNA is randomly broken into many small pieces, cloned into a bacterial host, and sequenced using chain termination. I am wondering - if we are having a gut microbiome sample and we break thos ...
gut sequencing written 5 months ago by fyfes30 • updated 5 months ago by antonioggsousa2.0k
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Kraken taxonomy sublevels
... Hi, Could you please tell me what does Kraken taxonomy sublevel mean? My output in taxonomy column is sometimes P (phylum) or sometimes P1 or P2. Thank you ...
kraken taxonomy taxonom written 6 months ago by fyfes30
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can standalone OMA be used on protein fasta (not genome)
... Hi, I have a group of proteins that I want to analyse if they are related, do you know if OMA can perform on only protein fasta as input? I am getting an error that I have provided 0 genomes so I am guessing it needs genomes as input but maybe there is an option to change the input many thanks! ...
orthologs oma written 9 months ago by fyfes30 • updated 9 months ago by adrian.altenhoff880
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CARD ID to UNIPROT ID
... Hello, I have some IDs from CARD database which are in GenBank format: ADH03009.1 AAA03550.1 AAC44793.1 CCP42991.1 AAB41701.1 CAC32082.1 BAM16262.1 Is there a way to mapp them directly to Uniprot? I have already tried uniprot programatic acces and online mapepr but id does not work. Many thanks! ...
uniprot card written 9 months ago by fyfes30 • updated 9 months ago by Sej Modha4.8k
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Comment: C: clustal omega distance matrix option
... thank you ...
written 9 months ago by fyfes30

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