enquiry: UCSC genome browser can't display my data

[Mariko Ozu]

Dear person in charge,

I am writing because your Genome browser didn't display my data after uploading it via Tools-Genome Graphs-upload box.
the data was in .bed format after processing NGS data (Rat RNAseq, fastq, originally), being named as 'rat_test' and 'rat_test1' when uploading, and produced from the tophat analysis.

It is so weird that even after min after uploading and after uploading there was sign of the completion of uploading and available sign on the web, the data weren't displayed on the Graph site at all.

Would you check what's wrong with the browser or your server?

Thank you for your assistance in advance.

best regards

Mariko Ozu, DVM

[Steve Heitner]

Hello, Mariko.

The Genome Graphs tool does not use BED format, but rather uses its own format.  From http://genome.ucsc.edu/cgi-bin/hgGenome, when you click the “upload” button, please carefully read the “Upload file formats” section just below the “Paste URLs or data” text box.

If you cannot supply your data in Genome Graphs format, you could create a custom track from your BED file in our Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables; see also http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html) and then use the “import” button in Genome Graphs to import your custom track.  Note that this will transform the track into Genome Graphs format with a certain window size and it might look different depending on the scale of view.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  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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Steve Heitner
UCSC Genome Bioinformatics Group

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