How to analyze RNA-seq mapping files (BAM files) for detection of all novel splicing events with type of change i.e. 5' or 3' alternative splice site. What I mean is that is there any tool or method available by which we can annotate novel splicing events present in entire transcriptome at global scale. For single gene or transcript this can be done by comparing assembled transcript to reference but what about high throughput RNA-Seq data containing thousands of transcripts?
You could start by looking at tophat and cufflinks. This tries to do this (tophat uses bowtie to generate bam files which are splice-aware).
scripture is another possibility. You have to be aware, that you need to look at the results very careful because it is not a easy job, and methods have their limitations. But cufflink, and scripture is an easy start.
@Jonathan Moore, Sir I had used tophat for alignment of reads. but is it possible by any tool for end to end comparison of exons in assembled transcripts and annotate each splicing event as 5' ar 3' splicing change, I mean simultaneously for all the splice sites present in all assembled transcripts?
Hi
I have worked in this direction. May be it will help you.
Here is the article.
A novel approach for accurate identification of splice junctions based on hybrid algorithms
I Mandal
Journal of Biomolecular Structure and Dynamic
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