User: David

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David50
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Posts by David

<prev • 28 results • page 1 of 3 • next >
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UniFrac in R with just the OTU table?
... Hi, I have an OTU table (not 16S data but WGS data from illumina). This table does not come from qiime. It´s a custom pipeline based on the taxonomy assignment using single copy genes (not 16S markers). I have build my OTU table i would like to compare samples using unifrac distances for example. I ...
phylogeny R metagenomics unifrac written 1 day ago by David50
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Answer: A: Get phylogenetic tree from abundance table
... Thanks guys for your comments and sorry for the confusion. Let me try to better explain. My data is WGS data (not 16S). What i call OTU (i know this is confusing corresponds to one species or lower rank (e.g order or phylum or class....) if resolution is lower) . Each OTU comes from a subset of my ...
written 1 day ago by David50
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Comment: A: Get phylogenetic tree from abundance table
... Sorry added the comment at the bottom ...
written 3 days ago by David50
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Comment: A: Get phylogenetic tree from abundance table
... thanks Philipps, Do you know if is possible to change the name of the ncbi ids in the tree. Although i will use the ncbi taxids to recover the tree i would like to to change the taxid in the output tree with an OTU id. For instance each row of my sample corresponds to a specific OTU , OTU_1, OTU_2 ...
written 4 days ago by David50
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Get phylogenetic tree from abundance table
... Hi, I have an abundance table (each row corresponds to a taxa). I would like to get the tree (newick default format) of the table. The table contains bacteria, archeae and fungi. How can i get a phylogenetic tree from this table (the original table has around 600 rows)?? The idea is to use the tree ...
phylogenetic ncbi newick written 4 days ago by David50
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Normalize bedtools gene coverage by total number of reads
... Hi, I have run a Hiseq 2x150bp from **metagenomics samples.** I have computed the gene coverage for a list of genes for a given sample. For each sample i take a subset of genes i´m interested in and mapped all reads to each of these genes generating a bam file that I use as input to bedtools as fo ...
bedtools normalization metagenomics written 6 days ago by David50
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Comment: C: Download NCBI genomes using taxonomy id (taxid)
... Hi i have noticed that the viral database [viral database assembly file][1] does only contain 3 viruses ??? [1]: ftp://ftp.ncbi.nih.gov/genomes/genbank/viral/ ...
written 26 days ago by David50
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Comment: C: Download NCBI genomes using taxonomy id (taxid)
... Yes i will use the assembly_summary file and get the wget links. Thanks ...
written 26 days ago by David50
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Comment: C: Download NCBI genomes using taxonomy id (taxid)
... In fact i have the taxonomy ID, not the species name !!! ...
written 26 days ago by David50
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Comment: C: Download NCBI genomes using taxonomy id (taxid)
... Great thanks, i´ll give it a try. ...
written 26 days ago by David50

Latest awards to David

Student 26 days ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)

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