Difference between revisions of "Bismark"
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|sw summary=Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion. | |sw summary=Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion. | ||
|bio domain=Epigenomics, Genomics | |bio domain=Epigenomics, Genomics | ||
| − | |bio method= | + | |bio method=Bisulfite mapping, Mapping, Methylation Calling |
|created by=Felix Krueger | |created by=Felix Krueger | ||
|created at=The Babraham Institute, Babraham Bioinformatics | |created at=The Babraham Institute, Babraham Bioinformatics | ||
Revision as of 16:22, 10 August 2010
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Application data |
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| Created by | Felix Krueger |
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| Biological application domain(s) | Epigenomics, Genomics |
| Principal bioinformatics method(s) | Bisulfite mapping, Mapping, Methylation Calling |
| Created at | The Babraham Institute, Babraham Bioinformatics |
| Maintained? | Yes |
| Input format(s) | FASTQ, FASTA |
| Output format(s) | custom Bismark output format |
| Software features | fast and convenient Bisulfite-Seq output, very flexible |
| Programming language(s) | Perl |
| Licence | GPLv3 |
| Operating system(s) | Linux |
Summary: Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.
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Bismark supports both single-end and paired-end read mapping of Bisulfite-Seq data in either fastA or fastQ format produced by e.g. the Illumina Genome Analyser IIx, while retaining much of the flexibility of Bowtie (adjust the seed length, number of mismatches, --best...). Sequence reads are first transformed into fully bisulfite-converted forward (C > T) and reverse reads (G > A conversion of the forward strand), before aligning them to similarly converted versions of the genome (also C>T and G>A). Sequence reads that produce a unique best alignment from the four alignment processes against the bisulfite genome (which are running in parallel), are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is determined.
Links
References
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