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Old 07-11-2015, 11:26 AM   #1
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Location: Cambridge, MA

Join Date: Jun 2015
Posts: 8
Default question about cufflinks masking

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.
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