Alternative Splicing Of Specific Region

Question

[Assa Yeroslaviz]

Hi,

I am looking for a method of analyzing the alternative splicing and/or different f transcript lengths of a specific gene in the mouse/human genomes.

I will download some published RNA-Seq data to do that.

What I would like to know is whether I need to do an analysis for the complete genome, or can I concentrate only on the specific region?

We presume that the gene has an alternative splice variants of two (or more ???) different length and would like to isolate this area and work only with it.

Is there any software to do so?

Can someone recommend a data base and/or software to do this kind of analysis?

Thanks for the help, Assa

[Arun]

might be silly, but, if you are looking at one gene, then why not do a northern blot and see the different transcripts (/isoforms) and get them sequenced?

[Arun]

because you are dealing with only one gene, isn't it possible to convert the isolated mRNA to cDNA and design specific primers and sequence the isoforms?

[Assa Yeroslaviz]

yes of course, it can be done. But first we need to know if there are any isoforms.

Answer 1

[Zheng Chen]

If you would like to use the public RNA-Seq data, my suggestion is still using the whole genome. When you just align all short reads to a specific loci, it is possible that some short reads generated from other loci can be sub-optimally mapped to your loci of interests, while those read should had a better match to its original loci.

To map RNA-seq reads to the genome, my recommendation is Tophat, which utilize Bowtie to map short reads to large genome while considering the splicing junctions between exons.