Difference between revisions of "GSNAP"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=GSNAP can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite treated DNA for the study of methylation state. | |sw summary=GSNAP can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite treated DNA for the study of methylation state. | ||
− | |bio domain=RNA-Seq | + | |bio domain=RNA-Seq alignment, DNA methylation, |
|bio method=Read mapping, Bisulfite mapping, | |bio method=Read mapping, Bisulfite mapping, | ||
|created at=Genentech | |created at=Genentech |
Latest revision as of 18:55, 2 December 2015
Application data |
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Biological application domain(s) | RNA-Seq alignment, DNA methylation |
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Principal bioinformatics method(s) | Read mapping, Bisulfite mapping |
Created at | Genentech |
Maintained? | Maybe |
Programming language(s) | C, Perl |
Summary: GSNAP can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite treated DNA for the study of methylation state.
"Error: no local variable "counter" was set." is not a number.
Limitations
- Does not seem to support color space.
Links
References
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