Difference between revisions of "SpliceMap"
m (Text replace - "RNA-Seq Alignment" to "RNA-Seq alignment") |
|||
| (2 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to improve mapping accuracy. | |sw summary=Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to improve mapping accuracy. | ||
| − | |bio domain=RNA-Seq | + | |bio domain=RNA-Seq alignment |
| − | |bio method= | + | |bio method=Read mapping, |
|created by=Kin Fai Au, John Mu | |created by=Kin Fai Au, John Mu | ||
|created at=Stanford University | |created at=Stanford University | ||
| Line 10: | Line 10: | ||
|os=Linux | |os=Linux | ||
}} | }} | ||
| − | + | ||
| + | = Limitations = | ||
| + | |||
| + | * Minimum read length is 50bp | ||
| + | * No color space support | ||
| + | |||
{{Links}} | {{Links}} | ||
{{References}} | {{References}} | ||
{{Link box}} | {{Link box}} | ||
Latest revision as of 19:04, 2 December 2015
|
Application data |
|
| Created by | Kin Fai Au, John Mu |
|---|---|
| Biological application domain(s) | RNA-Seq alignment |
| Principal bioinformatics method(s) | Read mapping |
| Created at | Stanford University |
| Maintained? | Yes |
| Output format(s) | SAM |
| Programming language(s) | Python, C++ |
| Operating system(s) | Linux |
Summary: Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to improve mapping accuracy.
"Error: no local variable "counter" was set." is not a number.
Limitations
- Minimum read length is 50bp
- No color space support
Links
References
To add a reference for SpliceMap, enter the PubMed ID in the field below and click 'Add'.
[ edit box ]
Search for "SpliceMap" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
