Getting Started
These steps will help you integrate IDP-fusion into your transcriptomics analysis pipeline.
- Read the IDP-fusion requirements for running IDP-fusion.
- Download and set-up the IDP-fusion package.
- Follow the guide for generating long read files suitable for isoform predicton or fusion detection.
- Follow the tutorial to see how IDP-fusion works on some example data.
- Read the manual if anything is unclear.
- You're ready, Happy IDPing!
Publication
Characterization of fusion genes and the significantly
expressed fusion isoforms in breast cancer by hybrid
sequencing.
Weirather, J.*, Afshar, P.T.*, Clark, T., Tseng, E., Powers, L., Underwood, J.G., Zabner, J., Korlach, J., Wong, W.H., Au, K.F.
Nucleic Acids Research. 2015 [Manuscript]
* These authors contributed equally to this work
IDP-fusion pipeline
This fusion-transcriptome is identified by the SpliceMap-LSC-IDP-fusion pipeline.
SpliceMap takes short reads from the Second Generation Sequencing platforms, such as Illumina, to detect exon junctions.
LSC makes use of the high-quality short reads to correct the long reads from PacBio platform. The output is the error-corrected long reads.
IDP-fusion uses the junction detections and the alignment of error-corrected long reads to detect the relatively short isoforms and fusion isforms at full-length and predict the very long isoforms and fusion isoforms by statistical modeling.
Latest News
01-19-2017 - Update to the IDP-fusion code.
This update addresses a number of bugs and troublesome issues with inpput files and segemenation faults when running STAR
10-24-2016 - Update to the IDP-fusion code
This update addresses compatability issues with newer versions STAR and GMAP aligners and other bug fixes.
02-12-2015 - First Upload of IDP-fusion code
This is a the first major release of IDP-fusion, and we will build a set of manuals and tutorials based on this release, then proceed to improve with updates as it becomes helpful to users.