Hello,
I would like to estimate the fraction of transcripts of a gene containing a given site (an exon, a domain, etc) out of all isoforms expressed in the sample. In the Wang Nature 2008 paper they introduced the inclusion ratio and percent spliced in concepts, which can fill this need. Alternatively, one can use something like cufflinks to measure the expression of each different isoform and use these values to measure how many of them contain the region of interest.
Are these approaches suitable, are there any other approaches, and which one could be better?
Thanks
I would like to estimate the fraction of transcripts of a gene containing a given site (an exon, a domain, etc) out of all isoforms expressed in the sample. In the Wang Nature 2008 paper they introduced the inclusion ratio and percent spliced in concepts, which can fill this need. Alternatively, one can use something like cufflinks to measure the expression of each different isoform and use these values to measure how many of them contain the region of interest.
Are these approaches suitable, are there any other approaches, and which one could be better?
Thanks