User: trichter

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trichter0
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Posts by trichter

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Answer: A: QIIME 1.9, make_phylogeny.py: Tree tips not preserved from fasta input
... To give another hint, the default treeing algorithm (-t fasttree) does provide the correct tree tips, while options "mafft" and "muscle" do not. ...
written 4 months ago by trichter0
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QIIME 1.9, make_phylogeny.py: Tree tips not preserved from fasta input
... Dear community, i am trying to build a tree with my representative OTU sequences for use with UniFrac. > align_seqs.py -i otus_min3.fa -m muscle -o muscle The first word of each fasta header in the input file starts with "OTU" and is preserved in the alignment. > head muscle/otus_min3_ali ...
sequencing alignment rna-seq qiime written 4 months ago by trichter0
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Comment: C: Normalization for NGS count data with high variance between observations / uneve
... Thank you, but our amplicons are all very similar in read lengths. It is the standard metagenomic 16S-survey. ...
written 19 months ago by trichter0
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Normalization for NGS count data with high variance between observations / uneven communities
... Dear group, we have a MiSeq 16S-dataset featuring samples from enrichment studies, i.e. communities from a time series in which some OTUs become dominant over time, e.g. up to 90% of all reads. The biological question would to find a) which OTUs respond to different enrichment strategies and b) whe ...
normalization next-gen written 19 months ago by trichter0 • updated 19 months ago by Asaf5.3k

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