Question: Displaying Bed Files In Ucsc
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gravatar for Xianrong Wong
6.2 years ago by
Xianrong Wong90 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
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ADD COMMENTlink modified 6.2 years ago by Jim Robinson150 • written 6.2 years ago by Xianrong Wong90
0
gravatar for Jim Robinson
6.2 years ago by
Jim Robinson150
Jim Robinson150 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.
ADD COMMENTlink written 6.2 years ago by Jim Robinson150
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 <
ADD REPLYlink written 6.2 years ago by Xianrong Wong90
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_dat a_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 To: "James Robinson" <jrobinso@broadinstitute.org> Cc: galaxy-user@lists.bx.psu.edu 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 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. 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
ADD REPLYlink written 6.2 years ago by Hiram Clawson260
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 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/
ADD REPLYlink written 6.2 years ago by Liz Ashley10
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 To: wongxr@gmail.com Cc: galaxy-user@lists.bx.psu.edu 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 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/
ADD REPLYlink written 6.2 years ago by Hiram Clawson260
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
ADD REPLYlink written 6.2 years ago by Xianrong Wong90
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_da ta_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 To: "Hiram Clawson" <hiram@soe.ucsc.edu> Cc: "Liz Ashley" <lizzilou@hotmail.com>, galaxy-user@lists.bx.psu.edu 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 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 To: wongxr@gmail.com Cc: galaxy-user@lists.bx.psu.edu 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 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/
ADD REPLYlink written 6.2 years ago by Hiram Clawson260
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