enquiry about the nature of mm9 mappability data

[Clarkson, Christopher T]

Hello,

I hope this is the right address to contact with concerns about the UCSC website-data. I downloaded a dataset from your "Table Browser" window with the following input parameters: "Mouse, Mapping and sequencing, zip file".

This was in an effort to find a measure of mappability throughout the genome (at bp level) and to align these measurements with a previous experiment output of GC content (also mapped to the genome at a nucleotide level), I want to plot and contrast GC content vs mappability.

However there is a problem with the zipped dataset that I downloaded. You can see from the screenshot of the unzipped bed file (attached) that certain nucleotides are skipped... Hence I can't map the mappability measurements to the GC contents as they won't align correctly... I am wondering why the file is organised this way.

If it is just the case that the skipped nucleotides have a mappability of 0 or 1, I can just fill in the gaps accordingly with a perl or python script...

Wondering if you could help clarify this for me.

Thanks,

Chris

[Cath Tyner]

Hello Chris,

Thank you for using the UCSC Genome Browser and for inquiring about these mappability data. In the screenshot that you sent, I see that there is one score for multiple positions in some cases, but I do not see an example of missing positions. Could you please clarify your question?

For reference, here is the track description page for Mappability,

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeMapability

Thank you again for your inquiry and for using the UCSC Genome Browser. 

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. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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