how does cufflinks cluster reads into a loci

[liuxq]

For some genomic loci, because the sequencing depth is not enough, reads located in the loci can not be tiled to each other to form a continuous region. However, i find that cufflinks can also assemble the transcript for these regions with sequencing gaps such as the following picture. How does cufflinks assemble gapped transcript? I do not find any parameter to control the allowed length of gap.

Thanks in advance and look forward to your response.