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The two tasks are quite different. Aligning means comparing sequences to find differences between them. Assembling means that you take a bunch of short sequences and try to stitch them back together to reconstitute the original DNA sequence. Fig1: Screen capture from DNA Baser Assembler of an 'assembly to reference'. The reference is in purple color. The ...


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Gene-1 Gene-2 Gene-3 Gene-1 100.00 16.18 20.35 Gene-2 16.18 100.00 29.66 Gene-3 20.35 29.66 100.00 Gene-1 and Gene-1 have 100% similarity (and all the other diagonal elements). Gene-1 and Gene-2 have 16.15% similarity, and so on. Therefore the matrix is symmetric M(i,j) = M(j,i). You can also show just the upper ...


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The use of RRBS instead of WGBS is mostly about coverage vs. cost. To confidently call methylation status at a cytosine residue, you need to have at least 10x sequencing coverage at that particular residue (ENCODE standards require at least 10x coverage for RRBS and 30x coverage for WGBS). To perform whole-genome bisulfite sequencing (WGBS) on large genomes ...



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