Cufflinks-Tophat-isoforms ?

[repinementer]

Hi guys

is it possible to extract isoforms of a single cell line with out comparing it to other cell lines by using Cufflinks & tophat ??

If it is possible how could I filter alternative splicing events like exon skipping and others?

(FYI: Cufflinks paper is over single cell line but different time points but my question just referring to a single cell line not any time points)

Thanx in advance

[AndrewCarpenter]

is it possible to extract isoforms of a single cell line with out comparing it to other cell lines by using Cufflinks & tophat ??

Yes, just use TopHat to align your reads. The aligned reads will be stored in the .sam file. Cufflinks will assemble mRNA isoforms based on this file.

If it is possible how could I filter alternative splicing events like exon skipping and others?

Cufflinks is used to estimate isoform expression. Isoforms are expressed due to alternative splicing events on pre-mRNA. So you would be saying that you wanted to filter out all the cufflinks output, therefore cufflinks would be useless to you.