User: David

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David50
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Posts by David

<prev • 36 results • page 1 of 4 • next >
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Comment: C: fastqc gc-content peak and adapter content
... Ok great. Yes I will start cleaning data. thanks ...
written 8 days ago by David50
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fastqc gc-content peak and adapter content
... Hi, I have the following fastqc profile and i´m just trying to understand what´s wrong with blue line. This is a human microRNA rna seq experiment (1x50bp) from human blood extracted microRNAs. In adapter content it starts around 18 (y axis) (small RNA 3´adapter). Why is that ?? Too much adapter ? ...
fastqc written 8 days ago by David50
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Comment: 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 4 weeks ago by David50
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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 4 weeks ago by David50
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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 4 weeks ago by David50
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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 8 weeks ago by David50
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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 8 weeks ago by David50
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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 8 weeks ago by David50
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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 8 weeks ago by David50
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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 8 weeks ago by David50

Latest awards to David

Student 4 weeks ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)
Student 12 weeks ago, asked a question with at least 3 up-votes. For Download NCBI genomes using taxonomy id (taxid)

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