Good Morning Noa:

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

--Hiram

----- Original Message ----- From: "Noa Sher" noa.sher@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

There are at least six of them there. Which one ?

----- Original Message ----- From: "Noa Sher" noa.sher@gmail.com To: "Hiram Clawson" hiram@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.sher@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

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.sher@gmail.com To: "Hiram Clawson" hiram@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.sher@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

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.sher@gmail.com To: "Hiram Clawson" hiram@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