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Forum: Bioinformatics 12-05-2012, 03:54 AM
Replies: 0
Views: 374
Posted By kenphi
Question cufflinks: Intron not within scaffold

Hi

I am using cufflinks 1.3.0 in --GTF-guide (-g) mode to do a guided de novo assembly. I get an extremely large number of "Warning: intron not within scaffold [(num, num), num]" warnings, e.g.:
...
Forum: Bioinformatics 02-24-2012, 01:48 AM
Replies: 3
Views: 1,722
Posted By kenphi
Dear silin I think this is because in your...

Dear silin

I think this is because in your reference annotation there are "unrelated" transcripts annotated to the same gene. I noticed that this happens, when there are independent transcript...
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