User: David

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David70
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Posts by David

<prev • 34 results • page 1 of 4 • next >
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Answer: A: Normalize bedtools gene coverage by total number of reads
... Hi, Couldn´t manage to get genes coverage using coverageCounts. It returns binary files. How would you get the gene coverage as numeric ? ...
written 20 hours ago by David70
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Comment: A: Normalize bedtools gene coverage by total number of reads
... Ok found it coverageCounts. Great I´ll normalize with Deseq2 , thanks ...
written 20 hours ago by David70
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Comment: A: Normalize bedtools gene coverage by total number of reads
... Thanks for your comments Carlo, Can you generate coverage using FeatureCounts from bam files ?? ...
written 20 hours ago by David70
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Comment: C: Normalization methods for metagenomics WGS data (not 16S data)
... I have a reads count table corersponding to a metagenomics experiment. I have cleared the reads (removed contaminants and filtered low quality reads). I have assigned taxonomy to the reads and build a table. Now i have a table (each column being a sample and each row being a taxa). I want to compar ...
written 25 days ago by David70
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Comment: A: Normalization methods for metagenomics WGS data (not 16S data)
... I have the table with read counts. What do you mean by reference to use ?? ...
written 25 days ago by David70
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Normalization methods for metagenomics WGS data (not 16S data)
... Hi, I have illumina 2x150 bp from a metagenomics experiment. This is not 16S data but WGS data. I was wondering if either DEseq2 or edgeR can be used for data normalization in this context ? I know these two are normally used for RNA data but it looks they might also perform well with DNA data (ba ...
normalization deseq2 edger written 25 days ago by David70
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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 28 days ago by David70
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Comment: 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 28 days ago by David70
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Comment: A: Get phylogenetic tree from abundance table
... Sorry added the comment at the bottom ...
written 4 weeks ago by David70
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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 weeks ago by David70

Latest awards to David

Student 20 hours ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)
Student 7 weeks ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)

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