User: allerdrengen55

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Posts by allerdrengen55

<prev • 22 results • page 1 of 3 • next >
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Normalizing gene counts in a quantitative metagenomic DNAseq analysis
... Hi! The purpose of my research, is to look at the gene abundance in a metagenomic sample (DNAseq). So it is not an expression analysis, since I am looking at genomic DNA. Furthermore, I am looking at different metagenomic samples, taken from different environments (specifically looking at bacteria) ...
illumina dna-seq count depth written 8 months ago by allerdrengen5520
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Comment: C: KEGG and metacyc database downloads
... It's a metagenomic sample. ...
written 8 months ago by allerdrengen5520
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Comment: C: KEGG and metacyc database downloads
... Thanks, I'll give it a shot. Though, I'm working with metagenomic data, so I have thousands of different organisms in my sample, and can't really filter any out. ...
written 8 months ago by allerdrengen5520
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Comment: C: KEGG and metacyc database downloads
... So there's no point in trying to convert EC to other IDs ? ...
written 8 months ago by allerdrengen5520
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KEGG and metacyc database downloads
... Hi! I have a file with a lot of eC_numbers. I would like to convert these numbers, so they represent KEGG and metacyc IDs instead. I need file where I can see what eC_numbers represent which KEGG/metacyc IDs. I also need a database of what the KEGG/metacyc IDs represent, enzyme-wise. I can't find ...
metacyc kegg download written 8 months ago by allerdrengen5520 • updated 8 months ago by Mark790
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Comment: C: Tools for visualization of taxonomic/gene/COG abundance in samples
... Thanks, I'll look into it! ...
written 8 months ago by allerdrengen5520
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Comment: C: Tools for visualization of taxonomic/gene/COG abundance in samples
... So there are basically two things Id like to compare between the samples: 1. Taxonomies. So the abundance of different bacteria in my samples. In the format: 34 Lactobacillus 93 E.Coli etc. I was thinking some sort of circle chart (like phylophlan). 2 Abundance of different COGs betwee ...
written 9 months ago by allerdrengen5520
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Tools for visualization of taxonomic/gene/COG abundance in samples
... Hi! I'm looking for tools that can help me visualize my data. I have 4 samples, in the same format. And I'm looking for a smart method of visualizing the comparison of the 4 samples in the same bar/plot/chart. I have tried with Phylophlan and Krona , but Phylophlan seemed a bit overkill (also hard ...
visualization cog abundance written 9 months ago by allerdrengen5520
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Comment: C: Mapping to contigs or predicted genes, for quantitative gene analysis (DNAseq)
... So there is no universal way to normalize my genes? My samples could potentially differ pretty much in terms of abundance of genes (levels?), so those tools won't be able to help? ...
written 9 months ago by allerdrengen5520
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Comment: C: Tool to extract COG information/description
... I just realized, that some COGs have multiple letters. Is that because the gene harbors both categories or because it doesn't know where to put it? ...
written 9 months ago by allerdrengen5520

Latest awards to allerdrengen55

Scholar 9 months ago, created an answer that has been accepted. For A: Using featureCount with a GFF file

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