How can I extract Alternative Splicing events from a set of transcripts?

Question

[mandana.baharlou]

Hi all,

I have a set of transcripts and I want to do AS analysis. Is there any tool or R package to do this?

thanks in advance,

[WouterDeCoster]

How did you obtain the data?

[mandana.baharlou]

My data set is a differentially expressed transcripts set.

[WouterDeCoster]

But not RNA-seq? Let me rephrase: which experimental method was used to obtain the data?

[mandana.baharlou]

I did RNA-seq analysis on short reads of two groups of samples(treated and control) then I did differential expression analysis and got my transcripts set. Now I want to detect AS events of my transcripts. Actually, I know there are many tools that do these tasks entirely but, I am searching for a tool that directly takes my transcripts as input.

[WouterDeCoster]

You would make things far easier by including this information in your initial posts from the beginning. Now we wasted quite some time to get basic information about your question. Please try to be as informative as possible when asking questions!

And why wouldn't you use existing tools for alternative splicing detection, e.g. MATS?

[mandana.baharlou]

As I said before I want to work straight with my transcripts. My data includes a set of transcript IDs and I want a method to find AS events of a specific transcript.

Answer 1

[natasha.sernova]

See this article, for example:

spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-81

Some other tools, but just several ones are R-packages :

https://omictools.com/alternative-splicing2-category

[mandana.baharlou]

Thank you for replying, but almost, all of these tools work with RNA-seq data whereas I am searching for a tool which takes transcripts as input.