I want to get Flux to simulate reads from different transcripts. So I am trying to understand how Flux deal with this situation. For example, if a gene has two isoforms. And an exon is absent in one isoform but present in the other. Those information are reflected in annotation file (gtf file). Therefore, how would Flux simulate reads which belong to that particular exon. Also will Flux generated reads across exon-exon boundary, this is to say the junction reads.
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Micha Sammeth
Hi Ruolin!
> if a gene has two isoforms. And an exon is absent in one isoform but present in the other. Those information are reflected in annotation file (gtf file).
That is right, the Simulator will assign expression levels to both (including and excluding the alternative exon in your example) transcripts, and if the transcript form including the alternative exon is expressed sufficiently high for, reads that cover the area of the exon are generated.
> Also will Flux generated reads across exon-exon boundary, this is to say the junction reads.
Sure, simulated reads can span one (or multiple) introns, i.e., they pop up as split-mappings.
Best,
Micha