Question: Alternative Splicing Of Specific Region
gravatar for Assa Yeroslaviz
7.6 years ago by
Assa Yeroslaviz1.2k
Assa Yeroslaviz1.2k wrote:


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

rna • 1.7k views
ADD COMMENTlink written 7.6 years ago by Assa Yeroslaviz1.2k

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?

ADD REPLYlink written 7.6 years ago by Arun2.3k

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?

ADD REPLYlink written 7.6 years ago by Arun2.3k

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

ADD REPLYlink written 7.5 years ago by Assa Yeroslaviz1.2k
gravatar for Zheng Chen
7.6 years ago by
Zheng Chen120
St. Louis
Zheng Chen120 wrote:

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.

ADD COMMENTlink written 7.6 years ago by Zheng Chen120
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1018 users visited in the last hour