Entering edit mode
8.0 years ago
2nelly
▴
310
Hi all,
I downloaded mm10 exons bed file from UCSC using the Table browser tool. The first bed is based on UCSC genes track and the second on refSeq tracks. The problem is that I noticed a huge difference in the total number of exons. The first one has 501841 and the second one 333021!
Does anybody have an idea what is going on?
thanks in advance!
Each annotation source will have different exons (they'll likely be largely overlapping).
Is it a strict exons file or a transcript bed file? UCSC may have some predicted transcripts that are not in refSeq.
Both files contain genes and genes predictions.ofc different annotation sources have different exons. But the difference here seems huge.
The various sources have drastically different thresholds for including a given transcript, so I guess we're not that surprised by this.