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My real question was if the size of the feature was measured in bases or kilo bases. I'm working with bacteria and the features are the kegg ontology, so that is why it puzzled me that most features was longer than an average genome, but now when I think about it would make even less sense if the size was measured in kb. Based on the raw and normalized counts I get the size of the K00001 feature to be 3.609.405 bases, can that be correct ?
onsdag den 20. januar 2021 kl. 10.20.50 UTC+1 skrev lu...@luispedro.org:That is correct: {normed} should divide by the size of the feature (note that the feature may be longer than a gene if you are not using seqname: it's the sum of the size of all the genes with a given annotation).I just also noticed that we never documented the fact that we also support {fpkm} (fragments per thousand per million fragments), but I added that bit to the documentation now.HTHLuisLuis Pedro Coelho | Fudan University | http://luispedro.orgOn Tue, 19 Jan 2021, at 9:39 PM, mette Joergensen wrote:HiIn the documentation for the count functions it says that the {normed} parameter results in the counts being divided by the size of the feature. Is the size of the feature measured in kb? I have an example where the raw count is around 3000 and the normalized value is around 0.0006 meaning that the gene should be more than 5MB long if the length is measured in bases. Or am I misunderstanding something?Best,Mette
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