All Gaps track for mm10

[Adrià Mitjavila]

Dear UCSC Genome Browser people, 

My name is Adrià Mitjavila. I am trying to compare different mouse strains and I need to search the assembly gaps for all these strains. 

I am using table browser for this and I have seen that for many mouse strains, e.g., NOD, there are two different gap tracks (see this link to table browser): 

• Gap (AGP)
• All Gaps

I am interested in the All Gaps track, since it contains all N bases, and for some genes, the "Gap (AGP)" does not contain all the gaps that appear in the sequence. 

Nevertheless, when looking at the reference mouse strain (mm10 genome) I can only find the "Gap (AGP)" track (see this link to table browser). 

Is there any difference between both annotations? And more importantly, why is the "All Gaps" track not present in the mm10 genome?

Thank you very much.

Best regards, 

Adrià Mitjavila Ventura

Bioinformatician

https://amitjavilaventura.github.io

[Gerardo Perez]

Hello, Adrià.

Thank you for your interest in the UCSC Genome Browser and for sending your inquiry.

We have added the All Gaps track to the mm10 genome browser:
https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&allGaps=dense

In short, the "All Gaps" track is a newer track that was implemented into genArk hubs and it has gaps in the assembly that have not been defined by the AGP file.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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