For your full 9-column GTF file, it is, as you have determined, tab-delimited
for the 9 columns.  In the ninth you can place any value tag pairs with
semi-colon ; delimiter.  Beware your excel produced file does not have
hidden characters that can upset the balance.  View your file in
an editor that can show the hidden characters, or on the command line:

cat -A yourFile.gtf | less

to see the hidden characters.  You should only see the 8 tab delimiters.

--Hiram

----- Original Message -----
From: "Noa Sher" <noa.s...@gmail.com>
To: "Hiram Clawson" <hi...@soe.ucsc.edu>
Cc: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 11:54:54 AM
Subject: Re: [galaxy-user] there was a wrong link in my previous mail - gtf 
file        issues



Hi Hiram, 

I managed to extract the columns in a different order (albeit I did it in excel 
and not using command line) but then the 9th column (attributes) of gtf is what 
I had problems with 

Thanks 

noa 
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