Tophat and cufflinks

[guzhi100]

Hi,

After mapping RNA-Seq reads with Tophat, I see reads mapped to non-exon regions.

My question is: will cufflinks take these reads when calculating gene/transcript expression level??????????

I hope not. Otherwise, the whole thing is not right.

Another question is; does anybody know where these "non-exon" reads come from????

Looking forward to your answers.

Thanks in advance.

[Jon_Keats]

depends on your cufflinks command. If you limit the analysis to a provided GTF you have the option to only count reads in the GTF space or the entire genome. For the most consistent result I limit the expression estimates to the GTF and only normalize to regions present in the GTF