Difference between revisions of "Cufflinks"
m (added type of read technology) |
m |
||
| Line 4: | Line 4: | ||
|bio method=Assembly, Differentially expressed gene identification, statistical testing, | |bio method=Assembly, Differentially expressed gene identification, statistical testing, | ||
|bio tech=Illumina, 454, Ion Torrent | |bio tech=Illumina, 454, Ion Torrent | ||
| − | |created at=University of Maryland, UC Berkeley, | + | |created by=Cole Trapnell |
| + | |created at=University of Maryland, UC Berkeley, Johns Hopkins University, | ||
| + | |maintained=Yes | ||
| + | |email address=tophat.cufflinks@gmail.com | ||
|input format=SAM, | |input format=SAM, | ||
|output format=GTF | |output format=GTF | ||
Revision as of 16:01, 16 September 2013
|
Application data |
|
| Created by | Cole Trapnell |
|---|---|
| Biological application domain(s) | RNA-Seq Alignment, RNA-Seq Quantitation, Differential Expression, Alternative Splicing, De novo transcriptome assembly, RNA-Seq |
| Principal bioinformatics method(s) | Assembly, Differentially expressed gene identification, statistical testing |
| Technology | Illumina, 454, Ion Torrent |
| Created at | University of Maryland, UC Berkeley, Johns Hopkins University |
| Maintained? | Yes |
| Input format(s) | SAM |
| Output format(s) | GTF |
| Licence | Boost |
| Contact: | tophat.cufflinks@gmail.com |
Summary: Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.
"Error: no local variable "counter" was set." is not a number.
Links
References
To add a reference for Cufflinks, enter the PubMed ID in the field below and click 'Add'.
[ edit box ]
Search for "Cufflinks" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
