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The primary product of protein coding genes are mRNAs. When we talk about measuring gene expression we want to assay the steady-state levels of a specific mRNA within a cell. This is usually accomplished by starting with a large number of cells and harvesting all of the mRNAs from all of the cells. One way to measure the expression level of just one ...


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According to next generation data: I was never working directly with mRNA but what I got from the bioinformatician was something like this: you extract your mRNA, sequence it, filter it according to the quality & length, assemble it and what you then have is something like "transcripts". Those you are counting: xy of transcript1 & yx of ...


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Adding to @David's answer, there has been some recent work looking at Neanderthal DNA in the context of Denisovan and modern human populations. David Reich's group [Sankararaman et al. Nature 2014] found Neanderthal-derived alleles in genes that affect skin and hair (specifically keratin filaments), as well as some that confer risk of disease. Another cool ...


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There was a very readable piece on this topic by Chris Stringer in Nature in 2012. At that time his general conclusion was: It is not yet clear whether the archaic DNA many of us carry is tied to any visible traits. Although he added: More controversially, some of the known differences in coding DNA between Neanderthals and recent humans are ...


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You're not wrong but gap can mean more than that. A good recent reference is this paper: Genetic variation and the de novo assembly of human genomes. Essentially, a gap occurs if something happens in our genome that can't be explained by uniformity. Since our genome is highly complicated, you can expect gap is also more than just mis-sequencing. The gap you ...


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The word ‘gap’ can be used both loosely and in specific genomic contexts, as listed by @Student T. The usage that seems to relate to your question — Sequence Coverage Gaps — is quite nicely illustrated in the Wikipedia entry on ‘Contig’. I reproduce, below, a modified form of a (public domain) illustration from it. The sequences of the ‘contigs’ (see ...


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I'm restricting this answer to Illumina. Even then, I don't know about the exact details of the raw data analysis (it is a proprietary software). Basically Illumina records the sequence based on photographic images. Each nucleotide has a distinct fluorescent label. In a cycle, a nucleotide is pumped and unincorporated nucleotides are washed off (this is ...


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While overlapping antisense RNAs are quite well known, there are very few examples in which both the RNAs from the pair can code for proteins. However, it is not impossible. I can cite one validated example: RU2S (DCDC2) and RU2AS (KAAG1) pair. While RU2S is constitutively and ubiquitously expressed, RU2AS is specifically expressed in kidney, bladder, ...


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I think this will vary greatly depending on the source environment. Your example (marine viruses) is probably due to the large diversity of ocean viruses of which most have no reference genome. Referencing the Human Microbiome Project: A total of 57.6% of the high-quality microbial reads could be associated with a known genome (ranging from 33–77% for ...


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In Drosophila, at least, some are clustered (e.g. these), but there are many tRNA genes in eukaryotes, so overall they are dispersed. You might find the Genomic tRNA Database useful, and the paper describing it.


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question looks like it's been dormant for a while, but i think there's some discussion to be had here- I would argue that in many (most?) of the model organisms, power would be much greater than humans. Frequently (worms, mice, plants, yeast) you can work with basically isogenic inbred lines. I would argue this is much more important than long haplotypes: ...



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