Question: How can I extract Alternative Splicing events from a set of transcripts?
0
gravatar for mandana.baharlou
2.5 years ago by
mandana.baharlou0 wrote:

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,

alternative splicing • 938 views
ADD COMMENTlink modified 2.5 years ago by natasha.sernova3.4k • written 2.5 years ago by mandana.baharlou0

How did you obtain the data?

ADD REPLYlink written 2.5 years ago by WouterDeCoster38k

My data set is a differentially expressed transcripts set.

ADD REPLYlink written 2.5 years ago by mandana.baharlou0

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

ADD REPLYlink written 2.5 years ago by WouterDeCoster38k

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.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by mandana.baharlou0

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?

ADD REPLYlink written 2.5 years ago by WouterDeCoster38k

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.

ADD REPLYlink written 2.5 years ago by mandana.baharlou0
0
gravatar for natasha.sernova
2.5 years ago by
natasha.sernova3.4k
natasha.sernova3.4k wrote:

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

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by natasha.sernova3.4k

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.

ADD REPLYlink written 2.5 years ago by mandana.baharlou0
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