Custom track viewing restricted by genome assembly version for S.cerevisiae

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Rege, Mayuri

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Jul 21, 2014, 11:48:15 AM7/21/14

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I am having trouble viewing a bedGraph file in the Genome browser depending on the genome assembly version I use.

The older assembly (sacCer1) of the yeast genome is the only one that I can view the track with.

The error I get with the newer assemblies (sacCer2 and sacCer3) is Error Unrecognized format type=bedGraph line 2 of custom track

Here is the start file:

track type=bedGraph name=Histone

chr1 11604 11896 1.49203

The release log from UCSC lists all three assemblies as available. How can this be fixed? Thank you!

-M Rege

Graduate student

University of Massachusetts Medical School

Worcester, MA

Luvina Guruvadoo

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Jul 21, 2014, 1:30:24 PM7/21/14

to Rege, Mayuri, gen...@soe.ucsc.edu

Hello Mayuri,

Thank you for your question. For both sacCer2 and sacCer3, the chromosomes are numbered using Roman numerals (i.e. chr"I" instead of chr"1"), which is why you are receiving the "Unrecognized format" error for those two assemblies. In the example you provided, I changed "chr1 11604 11896 1.49203" to "chrI 11604 11896 1.49203", and it uploaded successfully.

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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group