Hi Jen,
Thanks for your answer.
However, when I followed your instructions, I found that the forth column in my dataset, which is the expression level (or base depth covered by short read sequences), would be treated as names instead of values. Therefore I cannot see histogram on UCSC genome browser..
Could you help me more about the question? Thanks a lot!
Please see the following link to view my dataset.
http://main.g2.bx.psu.edu/u/johnwu/h/human-bodymap2
John Wu
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, August 05, 2011 10:16 PM To: 吳正華 Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] BedGraph format
Hello John,
A file in bedgraph format should display at UCSC. I think that #3 (below) is your concern, but there are a few things to check if the display at UCSC link is not showing up for the dataset:
1. File is tab delimited (not space or other) and four columns, such as (from the UCSC web site's example: http://genome.ucsc.edu/goldenPath/help/bedgraph.html):
chr19 59302000 59302300 -1.0 chr19 59302300 59302600 -0.75 chr19 59302600 59302900 -0.50 chr19 59302900 59303200 -0.25 chr19 59303200 59303500 0.0 chr19 59303500 59303800 0.25
2. Use "Edit Attributes" to assign a database (click on pencil icon in dataset). Confirm that this database is at UCSC by matching the database short name "dbkey" with that used in Galaxy. If the database is not at UCSC, then Visualization within Galaxy is still an option (Trackster). You can pull in other tracks from UCSC or other sources to view all of the data together for custom genomes.
3. Use "Edit Attributes" to also assign the file format as "bedgraph". The metadata will be automatically detected. The fourth column is not explicitly labeled as being a data value for display, but that does not impact display. Not all values for all datatypes are labeled the same as external sites do, yet many display correctly based on the file format type assigned.
4. Optional: create a track line using "Graph/Display Data -> Build custom track for UCSC genome browser". This is not necessary, but does allow for some user-defined labels. For full control over the track and (again, optional) browser lines used by UCSC, create this information in a text file on your computer, save, load into Galaxy, and merge with the bedgraph data using "Text Manipulation -> Concatenate datasets tail-to-head".
If this does not help and you are still having issues on the public Galaxy server at http://usegalaxy.org, please send a shared history link and I can take a look and provide feedback ("Options -> Share or Publish, generate link, and email back directly to me). But, hopefully the above helps to resolve anything that was unclear. I just tested a bedgraph a few minutes ago, to confirm that there were no issue between Galaxy & UCSC for a sample bedgraph dataset, and it worked fine.
Best!
Jen Galaxy team
On 8/4/11 9:01 PM, 吳正華 wrote:
Dear all:
I want to transform a text file to BedGraph format and show it on UCSC genome browser, but it seems that in galaxy I cannot assign a column that has values in configuration screen (BedGraph format).
How should I do the above task in galaxy?
Thanks
John Wu
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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
Hi,
I think you need to include a track line and specify "bedgraph", like this
track type=bedGraph
Is that maybe the problem? It sounds like UCSC is treating your file as a standard "bed", which it will do without the track line.
Jim
On Tue, Aug 9, 2011 at 11:32 PM, John Wu johnwu@ibms.sinica.edu.tw wrote:
Hi Jen,
Thanks for your answer.
However, when I followed your instructions, I found that the forth column in my dataset, which is the expression level (or base depth covered by short read sequences), would be treated as names instead of values. Therefore I cannot see histogram on UCSC genome browser..
Could you help me more about the question? Thanks a lot!
Please see the following link to view my dataset.
http://main.g2.bx.psu.edu/u/johnwu/h/human-bodymap2
John Wu
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, August 05, 2011 10:16 PM To: 吳正華 Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] BedGraph format
Hello John,
A file in bedgraph format should display at UCSC. I think that #3 (below) is your concern, but there are a few things to check if the display at UCSC link is not showing up for the dataset:
- File is tab delimited (not space or other) and four columns, such as (from the UCSC web site's example:
http://genome.ucsc.edu/goldenPath/help/bedgraph.html):
chr19 59302000 59302300 -1.0 chr19 59302300 59302600 -0.75 chr19 59302600 59302900 -0.50 chr19 59302900 59303200 -0.25 chr19 59303200 59303500 0.0 chr19 59303500 59303800 0.25
- Use "Edit Attributes" to assign a database (click on pencil icon in dataset). Confirm that this database is at UCSC by matching the database short name "dbkey" with that used in Galaxy. If the database is not at UCSC, then Visualization within Galaxy is still an option (Trackster).
You can pull in other tracks from UCSC or other sources to view all of the data together for custom genomes.
- Use "Edit Attributes" to also assign the file format as "bedgraph".
The metadata will be automatically detected. The fourth column is not explicitly labeled as being a data value for display, but that does not impact display. Not all values for all datatypes are labeled the same as external sites do, yet many display correctly based on the file format type assigned.
- Optional: create a track line using "Graph/Display Data -> Build custom track for UCSC genome browser". This is not necessary, but does allow for some user-defined labels. For full control over the track and (again, optional) browser lines used by UCSC, create this information in a text file on your computer, save, load into Galaxy, and merge with the bedgraph data using "Text Manipulation -> Concatenate datasets tail-to-head".
If this does not help and you are still having issues on the public Galaxy server at http://usegalaxy.org, please send a shared history link and I can take a look and provide feedback ("Options -> Share or Publish, generate link, and email back directly to me). But, hopefully the above helps to resolve anything that was unclear. I just tested a bedgraph a few minutes ago, to confirm that there were no issue between Galaxy & UCSC for a sample bedgraph dataset, and it worked fine.
Best!
Jen Galaxy team
On 8/4/11 9:01 PM, 吳正華 wrote:
Dear all:
I want to transform a text file to BedGraph format and show it on UCSC genome browser, but it seems that in galaxy I cannot assign a column that has values in configuration screen (BedGraph format).
How should I do the above task in galaxy?
Thanks
John Wu
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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Jim:
Thanks for your help!
I know how to make a bedgraph file, but it's just that I thought galaxy could automatically make a bedgraph file ( or track ) out from a text file.
Maybe I was thinking wrong.
John
-----Original Message----- From: James Robinson [mailto:jrobinso@broadinstitute.org] Sent: Wednesday, August 10, 2011 11:57 AM To: John Wu Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] BedGraph format
Hi,
I think you need to include a track line and specify "bedgraph", like this
track type=bedGraph
Is that maybe the problem? It sounds like UCSC is treating your file as a standard "bed", which it will do without the track line.
Jim
On Tue, Aug 9, 2011 at 11:32 PM, John Wu johnwu@ibms.sinica.edu.tw wrote:
Hi Jen,
Thanks for your answer.
However, when I followed your instructions, I found that the forth column
in my dataset, which is the expression level (or base depth covered by short read sequences), would be treated as names instead of values. Therefore I cannot see histogram on UCSC genome browser..
Could you help me more about the question? Thanks a lot!
Please see the following link to view my dataset.
http://main.g2.bx.psu.edu/u/johnwu/h/human-bodymap2
John Wu
-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, August 05, 2011 10:16 PM To: 吳正華 Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] BedGraph format
Hello John,
A file in bedgraph format should display at UCSC. I think that #3 (below) is your concern, but there are a few things to check if the
display at UCSC link is not showing up for the dataset:
- File is tab delimited (not space or other) and four columns, such as
(from the UCSC web site's example:
http://genome.ucsc.edu/goldenPath/help/bedgraph.html):
chr19 59302000 59302300 -1.0 chr19 59302300 59302600 -0.75 chr19 59302600 59302900 -0.50 chr19 59302900 59303200 -0.25 chr19 59303200 59303500 0.0 chr19 59303500 59303800 0.25
- Use "Edit Attributes" to assign a database (click on pencil icon in
dataset). Confirm that this database is at UCSC by matching the database short name "dbkey" with that used in Galaxy. If the database is not at UCSC, then Visualization within Galaxy is still an option (Trackster).
You can pull in other tracks from UCSC or other sources to view all of the
data together for custom genomes.
- Use "Edit Attributes" to also assign the file format as "bedgraph".
The metadata will be automatically detected. The fourth column is not
explicitly labeled as being a data value for display, but that does not impact display. Not all values for all datatypes are labeled the same as external sites do, yet many display correctly based on the file format type assigned.
- Optional: create a track line using "Graph/Display Data -> Build custom
track for UCSC genome browser". This is not necessary, but does allow for some user-defined labels. For full control over the track and (again, optional) browser lines used by UCSC, create this information in a text file on your computer, save, load into Galaxy, and merge with the bedgraph data using "Text Manipulation -> Concatenate datasets tail-to-head".
If this does not help and you are still having issues on the public Galaxy
server at http://usegalaxy.org, please send a shared history link and I can take a look and provide feedback ("Options -> Share or Publish, generate link, and email back directly to me). But, hopefully the above helps to resolve anything that was unclear. I just tested a bedgraph a few minutes ago, to confirm that there were no issue between Galaxy & UCSC for a sample bedgraph dataset, and it worked fine.
Best!
Jen Galaxy team
On 8/4/11 9:01 PM, 吳正華 wrote:
Dear all:
I want to transform a text file to BedGraph format and show it on UCSC genome browser, but it seems that in galaxy I cannot assign a column that has values in configuration screen (BedGraph format).
How should I do the above task in galaxy?
Thanks
John Wu
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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
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:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
galaxy-user@lists.galaxyproject.org
-
James Robinson -
John Wu