UCSC table browser, mappability, question regarding difference in input and output coordinates

[Hackenberg, Thomas]

Dear UCSC Team,

 

I am reaching out because of a question related to table browser, hg19, mapping and sequencing, mappability, CRG100

 

I queried a few regions (region of sequence homology), such as

chr4 20525637 20525800

to investigate problems with mappability.

 

The returned data (data points) is:

 

#bedGraph section chr4:20519963-20663312

chr4    20521582       20536643       1

 

The returned coordinates are not intersecting with the input and are several kb away (see bold highlights).

chrom	start.input	end.input	start.result	end.result	diff.start	diff.end
chr4	20525637	20525800	20521582	20536643	4055	10843

 

What is my mistake here?

Looking forward to your support.

Please reach out if you have questions.

 

Best

Thomas

 

Thomas Hackenberg Head of Product & Method Development Wet Lab thomas.h...@centogene.com CENTOGENE GmbH Am Strande 7 18055 Rostock Germany www.centogene.com
Management Board: Prof. Dr. Peter Bauer (CMGO), Miguel Coego Rios (CFO), Thomas Wiedermann (CRO) Registered seat: Rostock, registered with the commercial registers of the local court of Rostock under HRB 14967 Clinical accreditations: CLIA accredited: 99D2049715, CAP accredited: 8005167 This email and any files transmitted with it are confidential and may be legally privileged and are intended solely for the use of the individual or entity to whom they are addressed. If you are not the intended recipient please note that any disclosure, distribution or copying of this email is strictly prohibited and may be unlawful. If received in error, please delete this email and any attachments and inform the sender.

[Matthew Speir]

Hello, Thomas.

Thank you for your question about downloading data from the UCSC Table Browser.

The underlying data is in bedGraph format (stored as a bigWig file) which means that adjacent bases with the same value are merged into a single block. When you use the Table Browser to query these tracks and specify a position (or positions with the "define regions" option), it just looks for any items that overlap your input region. In this case, your input region falls in the middle of a larger region of bases with all the same value and so the Table Browser outputs that entire larger region. You can see this visually in this session where I've highlighted your input region and the output region: https://genome.ucsc.edu/s/mspeir/hg19_mappability_34586.

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.

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Matthew Speir

UCSC Genome Browser, User Support

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