User: mail2steff

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mail2steff60
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Potsdam, Germay
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Posts by mail2steff

<prev • 55 results • page 1 of 6 • next >
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How do I get the alignment score from multiple alignment in MAFFT
... Dear All, I have done multiple sequence alignment using mafft and got the alignment. But I could not get the alignment score for the MSA results. Where do I find alignment score for this?. I also tried t-coffee with the mafft-method. I got the same alignment as in Mafft website. I have attached the ...
multiple alignment t-coffee mafft written 9 weeks ago by mail2steff60
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Comment: C: Generating taxa-wise unifrac distance Matrix using phyloseq
... I searched found this: UniFrac distance and DPCoA cannot be calculated for taxa-wise distances, because they use a taxa-wise tree as part of their calculation between samples, and there is no transpose-equivalent for this tree. ...
written 3 months ago by mail2steff60
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Generating taxa-wise unifrac distance Matrix using phyloseq
... Dear All, I have OTU table obtained from qiime2 analysis and imported into phyloseq. I would like to get the unifrac distance between pair-wise species (not between the samples). in the output, I need distance matrix between the OTUs OTU1 OTU2 OTU3 OTU4 OTU5 OTU1 1 0.023 0 ...
R metagenomics phyloseq unifrac written 3 months ago by mail2steff60
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Comment: C: How do I calculate Jaccard distance between pair-wise OTUs species
... I forgot to change the method in the above post ...
written 3 months ago by mail2steff60
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Answer: A: How do I calculate Jaccard distance between pair-wise OTUs species
... I am sorry for the simple question I got it using following. > library(philentropy) > > compute the Jaccard Distance with default parameters > distance(x, method = "jaccard") ...
written 3 months ago by mail2steff60
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How do I calculate Jaccard distance between pair-wise OTUs species
... Dear All, I have OTU table obtained from qiime2 analysis. I would like to get the jaccard distance between pair-wise species (not between the samples). in the output, I need disatnce matrix between the OTUs > OTU1 OTU2 OTU3 OTU4 OTU5 > OTU1 1 0.023 0.045 0.12 0.034 ...
jaccard R metagenome written 3 months ago by mail2steff60
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How to combine two networks
... Dear All, I have two networks. Both the networks have common nodes as well as unique nodes. Is there any way I can combine both and analyze?? ...
network igraph cytoscape written 4 months ago by mail2steff60 • updated 3 months ago by zx87549.7k
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How to download the barcode sequences for particular study in HMP
... Dear All, I was able to download samples from the IBDMDB studies from Human Microbiome Project (HMP). But I wanted to get the meta data for those files especially primer and barcode sequences. How do I get those details? I also would like to know whether these data are already demultiplexed or Do we ...
hmp fastq microbiome human microbiome project written 9 months ago by mail2steff60
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Converting tab or txt file into gxl file using R programming
... Dear All, I have a tab delimited file with following columns > otu1 otu2 counts > OTU_1 OTU_2 0 > OTU_1 OTU_3 1 > OTU_1 OTU_4 1 : : : here otu1 is the source node and otu2 is the target node. count is the ...
gxl text r programming written 10 months ago by mail2steff60
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Comment: C: Increase the kmer size in IDBA_UD?
... Dear Sej Modha, Thank you for the commands. I increased the kmer value as above mentioned and the set the increment of k-mer of each iteration as 20. Eventhough I got the contigs for the kmwe 20, 40, 60, 80 and 100. Not more than that. Will IDBA_UD produce contigs upto 100 or AM I missing something ...
written 2.5 years ago by mail2steff60

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