Question: mm10 exons bed file
0
gravatar for 2nelly
3.0 years ago by
2nelly130
Athens
2nelly130 wrote:

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!

sequence gene • 1.6k views
ADD COMMENTlink written 3.0 years ago by 2nelly130
1

Each annotation source will have different exons (they'll likely be largely overlapping).

ADD REPLYlink written 3.0 years ago by Devon Ryan89k

Is it a strict exons file or a transcript bed file? UCSC may have some predicted transcripts that are not in refSeq.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax65k

Both files contain genes and genes predictions.ofc different annotation sources have different exons. But the difference here seems huge.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by 2nelly130

The various sources have drastically different thresholds for including a given transcript, so I guess we're not that surprised by this.

ADD REPLYlink written 3.0 years ago by Devon Ryan89k
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