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The BED (Browser Extensible Data) format is a text file format used to store genomic regions as coordinates and associated annotations. The data are presented in the form of columns separated by spaces or tabs. This format was developed during the Human Genome Project [1] and then adopted by other sequencing
For example, consider 9 contigs with the lengths 2,3,4,5,6,7,8,9, and 10; their sum is 54, half of the sum is 27, and the size of the genome also happens to be 54. Then, 50% of this assembly would be 10 + 9 + 8 = 27 (half the length of the sequence).
Sequence Alignment Map (SAM) is a text-based format originally for storing biological sequences aligned to a reference sequence developed by Heng Li and Bob Handsaker et al. [1] It was developed when the 1000 Genomes Project wanted to move away from the MAQ mapper format and decided to design a new format.
DNA extraction is the process of isolating DNA from the cells of an organism isolated from a sample, typically a biological sample such as blood, saliva, or tissue. It involves breaking open the cells, removing proteins and other contaminants, and purifying the DNA so that it is free of other cellular components.
The extensible NEXUS file format is widely used in phylogenetics, evolutionary biology, and bioinformatics.It stores information about taxa, morphological character states, DNA and protein sequence alignments, distances, and phylogenetic trees. [1]
The FAST4 format was invented as a derivative of the FASTQ format where each of the 4 bases (A,C,G,T) had separate probabilities stored. It was part of the Swift basecaller, an open source package for primary data analysis on next-gen sequence data "from images to basecalls". The FAST5 format was invented as an extension of the FAST4 format.
The package makes use of several tools: ShortRead (quality control), Bowtie, TopHat or BWA (alignment to a reference genome), SAMtools format, Cufflinks or MMSEQ (expression estimation). BioJupies is a web-based platform that provides complete RNA-seq analysis solution from free alignment service to a complete data analysis report delivered as ...
Flow chart for Hi-C data analysis. [29] Paired-end reads are first iteratively mapped to a reference genome. Mapped reads are then assigned to a restriction fragment/genomic loci, with fragment-level filtering. Data is then binned, filtered at the bin level, and then balanced to correct for potential biases. [29] [30]