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5

To get around limitations in using Venn diagrams for set overlaps, when there are more than three sets, back around 2013 or so I created something I called an Eulergrid plot (example at the bottom of the page), which an UpsetR plot appears to recapitulate, today. The Eulergrid code I wrote was in a mix of Perl and R; the UpsetR plot code uses R. There ...


4

Question 1: The additional sequences is needed because that is complimentary to the P5 sequence anchored to the flow cell. It is also the site for priming the Index 2 read on a MiSeq. The additional sequence is also needed for the read 1 primer in the cartridge to anneal to the correct place for the molecules. Question 2: The "GT" sequence you're referring ...


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The answer is in the supplementary methods page 3. Finally, all fragments in the same library with duplicate start and end coordinates were removed using Picard


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I ended up implementing the following greedy algorithm that should work fairly good for any binary relation even if it is not transitive nor symmetric. Assume you have the following binary relation (you may plug in any function you want): def does_a_cover_b(a,b, min_dist=30, max_dist=130): return min_dist < b.left_roi - a.left_end < max_dist or ...


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Module 3 does not exist during PCR amplification. Here is how NEBNext adaptor and multiplex PCR primers work. During the 1st PCR cycle, only the P7 primers are used to bind and amplify ligated DNA, generating the complementary strands that contain the binding sites for P5 primers (Universal in this case). During the second cycle of amplification, the P5 ...


1

The original point of the non-complementary sequence is to allow formation of a Y-adapter after USER treatment, since that's what's needed for the Illumina chemistry to work. In reality the bottom strand may not be there in step 3, since USER has already digested one strand (creating the hairpin in step 2) and size selection has been performed. Regardless, ...


1

I would stay away from using k-means, and instead use a method that doesn't a priori define a number of clusters to detect. It also looks as though your clusters aren't exactly spherical, which is an assumption of k-means. I personally am a fan of dbscan, which is available in the R package of the same name. The other poster recommended t-SNE (available in ...


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The basic equation for PCR kinetics (Equation 1) states that the amount of amplicon after c cycles (Nc) is the starting concentration of the amplicon (N0) times the amplification efficiency (E) to the power c. The PCR efficiency in this equation is a number between 1 and 2 (2 indicates 100% efficiency). NCBI In this article on research gate they said ...


1

This bash script will get you all of the reads that do not start with your primer sequence. It also handles degeneracy. It requires the tool bioawk. It works by looking at the first bases in the read and only prints out the headers that do not have a match with the degenerate primer. Then, comm makes sure that the read was retained in both the R1 and R2 ...


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