Re: There Was A Wrong Link In My Previous Mail

Question: Re: There Was A Wrong Link In My Previous Mail - Gtf File Issues

7.0 years ago by

Hiram Clawson • 260 wrote:

Good Morning Noa: Which one of the files at microbesonline are you trying to work with ? --Hiram To: galaxy-user@lists.bx.psu.edu 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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modified 7.0 years ago • written 7.0 years ago by Hiram Clawson • 260

7.0 years ago by

Hiram Clawson • 260

Hiram Clawson • 260 wrote:

There are at least six of them there. Which one ? To: "Hiram Clawson" <hiram@soe.ucsc.edu> Cc: galaxy-user@lists.bx.psu.edu 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 Good Morning Noa: Which one of the files at microbesonline are you trying to work with ? --Hiram 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

ADD COMMENT • link written 7.0 years ago by Hiram Clawson • 260

7.0 years ago by

Hiram Clawson • 260

Hiram Clawson • 260 wrote:

Is this the genome you are working with: http://archaea.ucsc.edu/cgi-bin/hgGateway?db=procMari_CCMP1375 To: "Hiram Clawson" <hiram@soe.ucsc.edu> Cc: galaxy-user@lists.bx.psu.edu 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 Good Morning Noa: Which one of the files at microbesonline are you trying to work with ? --Hiram 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

ADD COMMENT • link written 7.0 years ago by Hiram Clawson • 260

7.0 years ago by

Hiram Clawson • 260

Hiram Clawson • 260 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 To: "Hiram Clawson" <hiram@soe.ucsc.edu> Cc: galaxy-user@lists.bx.psu.edu 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 Good Morning Noa: Which one of the files at microbesonline are you trying to work with ? --Hiram 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

ADD COMMENT • link written 7.0 years ago by Hiram Clawson • 260

7.0 years ago by

Hiram Clawson • 260

Hiram Clawson • 260 wrote:

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 To: "Hiram Clawson" <hiram@soe.ucsc.edu> Cc: galaxy-user@lists.bx.psu.edu 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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