mm10 exons bed file

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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!

sequence gene • 3.7k views

ADD COMMENT • link 8.0 years ago by 2nelly ▴ 310

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

ADD REPLY • link 8.0 years ago by Devon Ryan 104k

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

ADD REPLY • link 8.0 years ago by GenoMax 141k

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

ADD REPLY • link 8.0 years ago by 2nelly ▴ 310

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

ADD REPLY • link 8.0 years ago by Devon Ryan 104k

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