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Arithmetic on a zero-based coordinate system is less complicated than that on a one-based system, so it appears zero-based is often (not exclusively) used for binary data formats, like BAM or bigBed, or text formats like BED, where computers are used to more efficiently calculate lengths of or set operations on intervals. A more complete answer on the ...


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"DNA data" comes in several forms dependent on the technology used to produce them. Companies like 23andMe are using SNP chips and those are available for an only rather a limited number of species. To be completely honest, I don't even know what would be the raw data they would provide, but I would suspect it could be a vcf file. If the chosen ...


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Maximal Unique Matches To answer the question about MUMs, there are two important definitions: A "match" is maximal if it cannot be extended in either direction and still be a match i.e, for two strings $s,r$, a match $s_i,...,s_{i+k}$, $r_{j},...,r_{j+k}$ is maximal if $s_i,...,s_{i+k+1}$, $r_{j},...,r_{j+k+1}$ is not a match and $s_{i-1},...,s_{...


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BCL (binary base call) files are the most raw data that you will likely get. As a matter of fact, the images taken by the machine each cycle are even more raw but it makes no sense to interact with this data directly. The base calls are derived from counting the spots (clusters) on the images. For any useful application you would convert them to fastq (e.g. ...


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Are you looking too far ahead into the future? No. This is certainly possible now. The gold standard being Illumina or BGI short read WGS. Long read sequencing can capture some extra data but is very noisy. How or where do one obtain such DNA data? There are now many companies. You want one the uses NGS with reads at least 150 bp and garantees at least a ...


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Consider mmJSON. Each of the three PDB sites had the same problem: using mmCIF files in web-based viewers is inefficient. To solve this problem three new file formats were introduced: MMTF at RCSB, BinaryCIF at PDBe, mmJSON at PDBj. MMTF has the smallest files – it's aggressively optimized for size. It is based on MessagePack, but on top of it uses a ...


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You can use PyMol to change the PDB to mmtf or other format. First open the PDB file and then choose file->export molecule-> choose which format you want to save as


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You can use qctool for this. If you create a list of IDs in list.txt (one ID per line), you can filter the .bgen file(s) by running qctool -g yourdata.bgen -s yourdata.sample -incl-samples list.txt -og yourdata_filtered.bgen


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