question about cufflinks masking

[asapp]

Hello all,

I recently created a merged.gtf file using cuffmerge. I want to mask all the known transcripts in this file when using cufflinks to search for novel transcripts at a particular locus (using the --mask-file <mask.gtf> option in cufflinks).

Here’s my question: can anyone tell me if --mask-file masks the entire transcript from assembly (i.e. from beginning to end irrespective of exon-intron structure) or just the identified exons, leaving the introns unmasked?

Thanks in advance for you help.
-Anna