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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