User: plicht

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plicht0
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Posts by plicht

<prev • 10 results • page 1 of 1 • next >
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Which diversity index for relative abundance data?
... Hi there, I have OTU tables as **relative** abundance data from MetaPhlAn. I am searching for emthods to calculate alpha diversity (richness and evenness). Most of the methods seem to require full counts which I ca nit provide with MetaPhlAn. I was trying phyloseq but the plot_richness function wan ...
R metagenomics statistics otu phyloseq written 1 day ago by plicht0
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Can I apply log transformation on proportions in compositional microbiomic data
... Hello, I have an abundance table with several samples as output from MetaPhlan, a classification tool for shotgun metagenomics data. From how the program is written, it can only tell you [relative abundances or proportions of taxa and not absolute counts][1]. However, I would like to test the R pac ...
selbal microbiome R compositional data written 7 days ago by plicht0
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How to normalize between samples in WGS metagenomics
... Hello, There is a big and increasing number of methods used for between sample normalization in whole genome metagenomics and yet no consensus which to apply [Normalization Methods][1]. Rarefaction is not a very suitable choice IMHO. Do you have experience with that? If sequencing depth does not ...
normalization metagenomics shotgun metagenomics written 4 months ago by plicht0
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Answer: A: How MetaPhlAn calculates relative abundance
... I guess the answer here is **(#reads of a bug mapping to marker / (size of clade_marker / clade_genome_size) * #total reads)**. But I am also confused by this. A clear equation would be nice. ...
written 4 months ago by plicht0
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Comment: C: what's meaning of parameter "-t rel_ab_w_read_stats"
... Could it be, that `-t rel_ab_w_read_stats` havn't been normalized to clade-marker coverage? But that would be in contrast to the name **relative** abundances with read stats. ...
written 4 months ago by plicht0
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Comment: A: Importing MetaPhlAn3 profile table into phyloseq to use decontam
... Hey c. e. chong, sorry for getting back so lately. Did you manage to get MetaPhlAn into Phyoloseq? Do you use total read counts (-t rel_ab_with_read_counts) or du you use relative abundances (-t rel_ab) when using the calculations in that package? Do you also plan to make use of Decontam? I guess ...
written 4 months ago by plicht0
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Trimmomatic on NEBNext Ultra II FS DNA
... Hello together, has anybody used Trimmomatic with the NEBNext Ultra II FS DNA Lib Prep Kit ([NEBNext Ultra II FS DNA][1]) together with Multiplex Oligos from NEB (e. g. [Multiplex Oligos for Illumina][2]) before? Do I need to adjust the reference adapter file of Trimmomatic? Since the adapters use ...
trimmomatic adapters next-gen sequencing written 5 months ago by plicht0
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Importing MetaPhlAn3 profile table into phyloseq to use decontam
... Hi there, I am new to R and would like to import the taxonomy profile table of MetaPhlAn3 into the R package phyloseq to make use of the package decontam. Therefore I merged several metaphlan analyses with the metaphlan internal command "merge_table". Then I imported the data into R using the rea ...
software error R written 5 months ago by plicht0
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Comment: C: Decontam data import (phyloseq?)
... Thanks a lot for the prompt answer! Here is an overview of the object merged_metaphlan > head(merged_metaphlan) clade_name NCBI_tax_id X1 X2 X5 1 UNKNOWN ...
written 5 months ago by plicht0 • updated 5 months ago by GenoMax95k
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Comment: A: Decontam data import (phyloseq?)
... Hey Antonio, I am alsy new to are and have troubles importing the MetaPhlAn3 output table as a phyloseq object to use that for the R package decontam. I merged several metaphlan analyses with the metaphlan internal command "merge_table". Then I imported the data into R using the read.table comman ...
written 5 months ago by plicht0 • updated 5 months ago by GenoMax95k

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