[galaxy-user] there was a wrong link in my previous mail - gtf file issues

2011-12-04 Thread Noa Sher 

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


Previous mail:
I am a non-programmer working on Prochlorococcus (a marine
  bacteria) for which UCSC and Ensembl do not yet have
  genome/transcriptome available or uploaded. However, the genome
  and transcriptome of this organism have been solved and annotated
  and are available on microbes online (http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=59919).

I have been trying to run transcriptome analyses using cufflinks,
  for which I need gtf files of the transcriptome. Microbes online
  has tab delimited files and I have been trying to convert them to
  gtf files using excel.  Basically, I reorganized the data so that
  the first 8 columns seem fine when uploaded to galaxy. The way I
  have been doing this is to save the file as a tab delimited excel
  file, and then upload the file onto Galaxy by "telling" galaxy
  that it is a gtf file (instead of allowing galaxy to identify the
  file type itself using the auto-detect function) when using the
  file upload option. However, when I do this, I cant get the 9th
  column (attributes) to work.
 I have tried either to separate the attributes in the 9th
  column in my excel spreadsheet by either a space or a tab (using
  concatenation with the char(9) function which I understand encodes
  a tab in excel). In all cases, when I upload to galaxy by
  identifying the .txt file as a .gtf file, the 9th column splits
  into columns 9,10,11, etc when I use a char(9) function in excel)
  or I get an error message from cufflinks (An error occurred
  running this job: cufflinks v1.0.3 cufflinks -q
--no-update-check -I 30 -F 0.05 -j 0.05 -p 8 -G
/galaxy/main_database/files/003/377/dataset_3377315.dat Error
running cufflinks. [Errno 2] No such file or directory:
'transcripts.gtf') when I use spaces to separate the
  attributes. 

I would be happy to know whether there is a way to convert my tab
delimited transcriptome file from Microbes Online to a gtf file
(either by excel or another program) which would enable me to use
galaxy's NGS functions on Prochlorococcus. 

Additionally, when I upload my data files I am able to choose the
prochlorococcus genome on galaxy (genome 213 in the 'upload file'
option), but am unable to chose it from the reference genome list
when performing tophat on galaxy. This may solve the problem (or
may be part of the same issue). 
Many thanks,
Noa Sher
  

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Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues

2011-12-04 Thread Hiram Clawson 

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

- 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 
fileissues

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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Galaxy analysis and other features on the public server
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Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues

2011-12-04 Thread Hiram Clawson 

Is this the genome you are working with:

http://archaea.ucsc.edu/cgi-bin/hgGateway?db=procMari_CCMP1375


- 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 
fileissues

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 
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
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Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues

2011-12-04 Thread Hiram Clawson 
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 
fileissues

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 
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

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Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues

2011-12-04 Thread Noa Sher 

  
  
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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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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