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


On 04/12/2011 21:43, Hiram Clawson wrote:
Pardon me, I see there is only one that says "tab-delimited" file.

That is a tough one to decode.  It almost looks like GTF already, but
not quite.  If we take it as a simple file of annotations on the genome,
without structure such as exons, introns, and merely rework the columns
to turn it into a bed file.  Extract columns in this order: 4,5,6,2,7
to get a bed file with the accession identities:

awk -F'\t' '{printf "%s\t%d\t%d\t%s\t%s\n", $4,$5,$6,$2,$7}' 59919.tab > 59919.bed

It would take some time to figure out how to convert this file
to something useful since I am not familiar with the format.
I can't see immediately how to use it properly.

--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 11:10:06 AM
Subject: Re: [galaxy-user] there was a wrong link in my previous mail - gtf file	issues

Hi Hiram, 

I was trying to work with the tab delineated file (using the link under export genomic data). 
Thanks 
noa 

On 04/12/2011 20:29, Hiram Clawson wrote: 

Good Morning Noa:

Which one of the files at microbesonline are you trying to work with ?

--Hiram

----- Original Message -----
From: "Noa Sher" <noa.s...@gmail.com> To: galaxy-user@lists.bx.psu.edu Sent: Sunday, December 4, 2011 1:38:35 AM
Subject: [galaxy-user] there was a wrong link in my previous mail - gtf file	issues




The correct link: http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=59919 
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