Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments are(based on the start and end coordinates) with numerical scores beside each fragment. How do I view the file as a histogram format? What format will I need to convert the file to and where can I do the conversion? Any advise is greatly appreciated! Jose
Hi Jose, What you have described is a "bedgraph" file. Perhaps changing the file extension to "bedgraph" will be enough, if not you might be required to enter a track line. See UCSC for details. On Thu, May 10, 2012 at 9:04 PM, Xianrong Wong <wongxr@gmail.com> wrote:
Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments are(based on the start and end coordinates) with numerical scores beside each fragment. How do I view the file as a histogram format? What format will I need to convert the file to and where can I do the conversion? Any advise is greatly appreciated!
Jose ___________________________________________________________ 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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I changed it to bedgraph and can no longer view in UCSC (the button to view in UCSC was not there anymore). I had it in bed format subsequently and put in a header. I was looking at the bedgraph/wiggle header documentation on UCSC but don't find any that describes displaying scores in histogram format. I saw that we can change colour the intensity of the bars based on scores though. Jose On Thu, May 10, 2012 at 10:27 PM, James Robinson < jrobinso@broadinstitute.org> wrote:
Hi Jose,
What you have described is a "bedgraph" file. Perhaps changing the file extension to "bedgraph" will be enough, if not you might be required to enter a track line. See UCSC for details.
On Thu, May 10, 2012 at 9:04 PM, Xianrong Wong <wongxr@gmail.com> wrote:
Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments are(based on the start and end coordinates) with numerical scores beside each fragment. How do I view the file as a histogram format? What format will I need to convert the file to and where can I do the conversion? Any advise is greatly appreciated!
Jose ___________________________________________________________ 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
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Good Evening Jose: Please note the types of graphing formats you can display at UCSC: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format I would recommend converting your bedgraph file to a bigWig file and display that via a remote URL. This would be your most efficient mechanism of display. --Hiram ----- Original Message ----- From: "Xianrong Wong" <wongxr@gmail.com> To: "James Robinson" <jrobinso@broadinstitute.org> Cc: galaxy-user@lists.bx.psu.edu Sent: Thursday, May 10, 2012 9:27:07 PM Subject: Re: [galaxy-user] Displaying bed files in ucsc I changed it to bedgraph and can no longer view in UCSC (the button to view in UCSC was not there anymore). I had it in bed format subsequently and put in a header. I was looking at the bedgraph/wiggle header documentation on UCSC but don't find any that describes displaying scores in histogram format. I saw that we can change colour the intensity of the bars based on scores though. Jose On Thu, May 10, 2012 at 10:27 PM, James Robinson < jrobinso@broadinstitute.org > wrote: Hi Jose, What you have described is a "bedgraph" file. Perhaps changing the file extension to "bedgraph" will be enough, if not you might be required to enter a track line. See UCSC for details. On Thu, May 10, 2012 at 9:04 PM, Xianrong Wong < wongxr@gmail.com > wrote: Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments are(based on the start and end coordinates) with numerical scores beside each fragment. How do I view the file as a histogram format? What format will I need to convert the file to and where can I do the conversion? Any advise is greatly appreciated! Jose
In the title information you need to include UseScore information including the range you want to cover with your histogram. There is a section in the UCSC website that explains the content: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 For stating the range of your histogram: scoreMin=X scoreMax=X. This will mean that the greyscale shading uses the two X values as the value for white and black, all other points will be an even range like the example on the UCSC browser page. When I was doing this the information I used was wiggle format: track type = wiggle_0 name="name of track" description="description" useScore=1 scoreMin=0 scoreMax=6. ChrNo StartPos FinishPos Score Hope that makes sense/helps lizzy On Thu, May 10, 2012 at 9:04 PM, Xianrong Wong <wongxr@gmail.com> wrote: Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments are(based on the start and end coordinates) with numerical scores beside each fragment. How do I view the file as a histogram format? What format will I need to convert the file to and where can I do the conversion? Any advise is greatly appreciated! Jose ___________________________________________________________ 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: http://lists.bx.psu.edu/ ___________________________________________________________ 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: http://lists.bx.psu.edu/
Please note the arguments you can use in a track line for a type=wiggle_0 format file: http://genome.ucsc.edu/goldenPath/help/wiggle.html The arguments useScore, scoreMin, scoreMax have no meaning with a wiggle track. A wiggle track does not display items in a gray-scale fashion, it draws a graph of the data values. --Hiram ----- Original Message ----- From: "Liz Ashley" <lizzilou@hotmail.com> To: wongxr@gmail.com Cc: galaxy-user@lists.bx.psu.edu Sent: Friday, May 11, 2012 6:05:14 AM Subject: Re: [galaxy-user] Displaying bed files in ucsc In the title information you need to include UseScore information including the range you want to cover with your histogram. There is a section in the UCSC website that explains the content: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 For stating the range of your histogram: scoreMin=X scoreMax=X. This will mean that the greyscale shading uses the two X values as the value for white and black, all other points will be an even range like the example on the UCSC browser page. When I was doing this the information I used was wiggle format: track type = wiggle_0 name="name of track" description="description" useScore=1 scoreMin=0 scoreMax=6. ChrNo StartPos FinishPos Score Hope that makes sense/helps lizzy On Thu, May 10, 2012 at 9:04 PM, Xianrong Wong < wongxr@gmail.com > wrote: Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments are(based on the start and end coordinates) with numerical scores beside each fragment. How do I view the file as a histogram format? What format will I need to convert the file to and where can I do the conversion? Any advise is greatly appreciated! Jose ___________________________________________________________ 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: http://lists.bx.psu.edu/ ___________________________________________________________ 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: http://lists.bx.psu.edu/ ___________________________________________________________ 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: http://lists.bx.psu.edu/
Thank you for the advise. I am able to view now when I use track type=wiggle_0 but I can only do it a few chr at a time which is good enough. Just curious, what track type do I type in when I want it to be bedgraph? It seems the _0 was important for wiggle. Jose On Fri, May 11, 2012 at 9:34 AM, Hiram Clawson <hiram@soe.ucsc.edu> wrote:
Please note the arguments you can use in a track line for a type=wiggle_0 format file:
http://genome.ucsc.edu/goldenPath/help/wiggle.html
The arguments useScore, scoreMin, scoreMax have no meaning with a wiggle track. A wiggle track does not display items in a gray-scale fashion, it draws a graph of the data values.
--Hiram
----- Original Message ----- From: "Liz Ashley" <lizzilou@hotmail.com> To: wongxr@gmail.com Cc: galaxy-user@lists.bx.psu.edu Sent: Friday, May 11, 2012 6:05:14 AM Subject: Re: [galaxy-user] Displaying bed files in ucsc
In the title information you need to include UseScore information including the range you want to cover with your histogram. There is a section in the UCSC website that explains the content: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
For stating the range of your histogram: scoreMin=X scoreMax=X. This will mean that the greyscale shading uses the two X values as the value for white and black, all other points will be an even range like the example on the UCSC browser page.
When I was doing this the information I used was wiggle format: track type = wiggle_0 name="name of track" description="description" useScore=1 scoreMin=0 scoreMax=6. ChrNo StartPos FinishPos Score
Hope that makes sense/helps lizzy
On Thu, May 10, 2012 at 9:04 PM, Xianrong Wong < wongxr@gmail.com > wrote:
Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments are(based on the start and end coordinates) with numerical scores beside each fragment. How do I view the file as a histogram format? What format will I need to convert the file to and where can I do the conversion? Any advise is greatly appreciated!
Jose
___________________________________________________________ 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:
___________________________________________________________ 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: http://lists.bx.psu.edu/ ___________________________________________________________ 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:
With your setting of type=wiggle_0 and using bedGraph format, you happen to have selected the most inefficient mechanism of displaying this data as explained here: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format That's the reason why you can only see a few chromosomes of data. The immense amount of data in your file cannot survive the transfer time-out. You could get a little better performance with type=bedGraph: http://genome.ucsc.edu/goldenPath/help/bedgraph.html See also: http://genome.ucsc.edu/goldenPath/help/customTrack.html However, in order to see all of your data you must use the bigWig format. I'm sure there is a bedGraph to bigWig conversion function at galaxy. Use that function and then submit a single track line to describe the data options and specify the bigDataUrl to your bigWig format file. This will save you much time and trouble. http://genome.ucsc.edu/goldenPath/help/bigWig.html --Hiram ----- Original Message ----- From: "Xianrong Wong" <wongxr@gmail.com> To: "Hiram Clawson" <hiram@soe.ucsc.edu> Cc: "Liz Ashley" <lizzilou@hotmail.com>, galaxy-user@lists.bx.psu.edu Sent: Friday, May 11, 2012 1:42:37 PM Subject: Re: [galaxy-user] Displaying bed files in ucsc Thank you for the advise. I am able to view now when I use track type=wiggle_0 but I can only do it a few chr at a time which is good enough. Just curious, what track type do I type in when I want it to be bedgraph? It seems the _0 was important for wiggle. Jose On Fri, May 11, 2012 at 9:34 AM, Hiram Clawson < hiram@soe.ucsc.edu > wrote: Please note the arguments you can use in a track line for a type=wiggle_0 format file: http://genome.ucsc.edu/goldenPath/help/wiggle.html The arguments useScore, scoreMin, scoreMax have no meaning with a wiggle track. A wiggle track does not display items in a gray-scale fashion, it draws a graph of the data values. --Hiram ----- Original Message ----- From: "Liz Ashley" < lizzilou@hotmail.com > To: wongxr@gmail.com Cc: galaxy-user@lists.bx.psu.edu Sent: Friday, May 11, 2012 6:05:14 AM Subject: Re: [galaxy-user] Displaying bed files in ucsc In the title information you need to include UseScore information including the range you want to cover with your histogram. There is a section in the UCSC website that explains the content: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 For stating the range of your histogram: scoreMin=X scoreMax=X. This will mean that the greyscale shading uses the two X values as the value for white and black, all other points will be an even range like the example on the UCSC browser page. When I was doing this the information I used was wiggle format: track type = wiggle_0 name="name of track" description="description" useScore=1 scoreMin=0 scoreMax=6. ChrNo StartPos FinishPos Score Hope that makes sense/helps lizzy On Thu, May 10, 2012 at 9:04 PM, Xianrong Wong < wongxr@gmail.com > wrote: Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments are(based on the start and end coordinates) with numerical scores beside each fragment. How do I view the file as a histogram format? What format will I need to convert the file to and where can I do the conversion? Any advise is greatly appreciated! Jose ___________________________________________________________ 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: http://lists.bx.psu.edu/ ___________________________________________________________ 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: http://lists.bx.psu.edu/ ___________________________________________________________ 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: http://lists.bx.psu.edu/
participants (4)
-
Hiram Clawson -
James Robinson -
Liz Ashley -
Xianrong Wong