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Old 05-09-2011, 06:10 PM   #1
Hunny
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Location: Beijing, China

Join Date: Apr 2011
Posts: 23
Default One problem about RefSeq annotation file

Hi Guys,

I have one question about the RefSeq annotation file downed from UCSC.

Take the mm9 as example,

Firstly, I downloaded the RefSeq GTF file of mm9 genome from the UCSC website and named it mm9_RefSeq.

Then I wanted to see if the file format is standard, so I uploaded the file, namely mm9_RefSeq to the UCSC again. But an error jumped out with

'Error File 'mm9_RefSeq' - GFF/GTF group NM_001031622_dup2 on chr5_random-, this line is on chrUn_random+, all group members must be on same seq and strand'

As I didn't know much about either chrUn_ramdom or chrN_ramdom, I searched them and found them on the UCSC FAQ board,
http://genome.ucsc.edu/FAQ/FAQdownloads.html

So my question is should I delete the entries referring to chrUn_ramdom and chrN_ramdom from the standard RefSeq annotation file before uploading it to the UCSC genome browser?

And I also wanted to know what information could be observed from the chrUn_ramdom and chrN_ramdom entries in mm9_RefSeq. Could anybody please give me some ideas about it?

Thanks a lot,
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