One problem about RefSeq annotation file

Hunny · 05-09-2011, 06:10 PM

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,

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
GFF Annotation file	AAWT	Bioinformatics	3	12-12-2012 12:58 AM
Annotation File	mattia	Bioinformatics	0	11-25-2011 02:24 AM
read annotation problem	StephaniePi83	Bioinformatics	0	11-24-2011 09:30 AM
pileup file annotation	NM_010117	Bioinformatics	4	02-16-2011 02:49 PM
genome annotation problem	dicty	Bioinformatics	0	02-07-2011 07:30 AM

05-09-2011, 06:10 PM	#1
Hunny Member Location: Beijing, China Join Date: Apr 2011 Posts: 23	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,