User: plicht
plicht • 0
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Posts by plicht
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... 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 ...
written 1 day ago by
plicht • 0
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... 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 ...
written 7 days ago by
plicht • 0
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... 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 ...
written 4 months ago by
plicht • 0
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... 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
plicht • 0
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... 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
plicht • 0
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... 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
plicht • 0
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... 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 ...
written 5 months ago by
plicht • 0
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... 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 ...
written 5 months ago by
plicht • 0
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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 ...
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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 ...
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