Has anyone come across some software that can identify either novel or differential splicing events within or between RNA-seq libraries?
I am not sure if you can use this software to compare between libraries, but a software I've used to detect gene splicing site is GeneSplicer.
I am looking for something that uses short read RNA sequencing data (RNA-seq) to identify novel splicing events in a given sample or, if multiple samples are available, identifies differential splicing events between those samples.
I figured it was something a little more complicated than a simple splice-site search :). Good luck finding an application that can do this. It is definitely beyond my expertise.
Yes. So complicated, in fact, that I probably have to wait for such a tool to be developed... or to develop it myself.
Hi Ryan, I know that this post is old but I wondered if you found a software that can identify differential splicing between two conditions? Or maybe if you had a solution to compare your data?
I used tophat to align my reads and to identify splice junctions but now i would like to be able to compare my two conditions.
A colleague of mine wrote some software that does this. I will ask him to comment on this thread.
I have been working on a method for this. Currently the method is still under development and the manuscript is in review. As a starting point, you can check out our website for a description of the method and see examples of what we produce as output:
thanks for the answer
Your work seems very interesting and I hope that your paper will be accepted soon to be able to use your software!
It's too bad to have rna seq datas and not be able to have an answer for alternatively spliced genes!
And I would like to know if your software is compatible with tophat output? or do you need some special format from a specific aligner?
Is the software identifying novel splice form or differential splice events available now?