New answers tagged sequence-analysis
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 ...
Clustal has reinvented itself as Clustal Omega using Hidden Markov Models, and is particularly suited to the alignment of very many sequences.
The FTP download files are documented on the UCSC site (from which they also may be downloaded from a web browser). The page for the human genome is http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/. I don't know which files you downloaded, but I quote three of the descriptions: hg38.2bit - contains the complete human/hg38 genome sequence in ...
The IUPAC Nomenclature symbol table for RNA and DNA nucleotide sequences (via Wikipedia)
Lowercase letters indicate repeat-masked regions. N's represent gaps. See: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/S4Sx8UdJAwM/tLTpVVzdhFMJ
Sequence in caps are usually regions of interest, such as exons. N in the DNA alphabet refers to "unknown nucleotide" It can refer to any of A/T/C/G when the actual underlying base is unknown.
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 ...
The applications for counting the k-mer occurences in a sequence are: building de Bruijn graphs  for de novo assembly from very large number of short reads, produced by next generation sequencing, fast multiple sequence alignment , and  repeat detection. Compeau PE, Pevzner PA, Tesler G: How to apply de Bruijn graphs to genome assembly. ...
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