Re: [galaxy-user] Help!!! cuffdiff log2 value
Hi Jiwen, As far as I know, this is possible. The CuffDiff log2 value is defined here: http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff 7 FPKMx 8.01089 FPKM of the gene in sample x 8 FPKMy 8.551545 FPKM of the gene in sample y 9 log2(FPKMy/FPKMx) 0.06531 The (base 2) log of the fold change y/x And log(2) in general (including a graph, which can help with visualizing) is described here (although the web is full if similar): http://en.wikipedia.org/wiki/Logarithm I can see that this same Q on seqanswers.com recieved pretty much the same answer (in brief! http://seqanswers.com/forums/showthread.php?t=19558), so I think you are safe using the data as it as generated. Taking a look at the inputs would be advised if the results were unexpected. If you do still have concerns about the log(2) calculation, asking the tool authors directly (if you have't done so already) at tophat.cuffli...@gmail.com is always an option, to tripple check. Best, Jen Galaxy team On 4/26/12 7:48 AM, 杨继文 wrote: Hi, I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of differentially expressed transcrpts or genes. As far as I know, log2 value = fold change. However, there are minus values. Is this possible?? log2 value can not be minus. Did I miss something?? Looking forward to your help. Thanks in advance. Best Jiwen 网易Lofter，专注兴趣，分享创作！ http://www.lofter.com ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
Re: [galaxy-user] Help!!! cuffdiff log2 value
I think the sign is to show if it is x-fold more than the first condition (+) or x-fold less than the first condition (-). A regular fold would give you values from 1-whatever if sample 2 is more than sample 1, and a fraction (0-1) if sample 1 is expressed more than sample 2. The log lets you get both on the same scale, so that 2 means (on log2 scale) four-fold upregulated, and -2 means four-fold downregulated. FPKM x FPKM y y/x log(y/x) 1 2 2 1 1 0.5 0.5 -1 On 10/05/2012 19:00, Jennifer Jackson wrote: Hi Jiwen, As far as I know, this is possible. The CuffDiff log2 value is defined here: http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff 7 FPKMx 8.01089 FPKM of the gene in sample x 8 FPKMy 8.551545 FPKM of the gene in sample y 9 log2(FPKMy/FPKMx) 0.06531 The (base 2) log of the fold change y/x And log(2) in general (including a graph, which can help with visualizing) is described here (although the web is full if similar): http://en.wikipedia.org/wiki/Logarithm I can see that this same Q on seqanswers.com recieved pretty much the same answer (in brief! http://seqanswers.com/forums/showthread.php?t=19558), so I think you are safe using the data as it as generated. Taking a look at the inputs would be advised if the results were unexpected. If you do still have concerns about the log(2) calculation, asking the tool authors directly (if you have't done so already) at tophat.cuffli...@gmail.com is always an option, to tripple check. Best, Jen Galaxy team On 4/26/12 7:48 AM, 杨继文 wrote: Hi, I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of differentially expressed transcrpts or genes. As far as I know, log2 value = fold change. However, there are minus values. Is this possible?? log2 value can not be minus. Did I miss something?? Looking forward to your help. Thanks in advance. Best Jiwen 网易Lofter，专注兴趣，分享创作！ http://www.lofter.com ___ 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/
Re: [galaxy-user] Help!!! cuffdiff log2 value
Hi Noa, This is it exactly - thanks for adding in the interpretation! Jen On 5/10/12 11:54 AM, Noa Sher wrote: I think the sign is to show if it is x-fold more than the first condition (+) or x-fold less than the first condition (-). A regular fold would give you values from 1-whatever if sample 2 is more than sample 1, and a fraction (0-1) if sample 1 is expressed more than sample 2. The log lets you get both on the same scale, so that 2 means (on log2 scale) four-fold upregulated, and -2 means four-fold downregulated. FPKM x FPKM y y/x log(y/x) 1 2 2 1 1 0.5 0.5 -1 On 10/05/2012 19:00, Jennifer Jackson wrote: Hi Jiwen, As far as I know, this is possible. The CuffDiff log2 value is defined here: http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff 7 FPKMx 8.01089 FPKM of the gene in sample x 8 FPKMy 8.551545 FPKM of the gene in sample y 9 log2(FPKMy/FPKMx) 0.06531 The (base 2) log of the fold change y/x And log(2) in general (including a graph, which can help with visualizing) is described here (although the web is full if similar): http://en.wikipedia.org/wiki/Logarithm I can see that this same Q on seqanswers.com recieved pretty much the same answer (in brief! http://seqanswers.com/forums/showthread.php?t=19558), so I think you are safe using the data as it as generated. Taking a look at the inputs would be advised if the results were unexpected. If you do still have concerns about the log(2) calculation, asking the tool authors directly (if you have't done so already) at tophat.cuffli...@gmail.com is always an option, to tripple check. Best, Jen Galaxy team On 4/26/12 7:48 AM, 杨继文 wrote: Hi, I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of differentially expressed transcrpts or genes. As far as I know, log2 value = fold change. However, there are minus values. Is this possible?? log2 value can not be minus. Did I miss something?? Looking forward to your help. Thanks in advance. Best Jiwen 网易Lofter，专注兴趣，分享创作！ http://www.lofter.com ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
[galaxy-user] default data for a tool
Hi, Is there a way to specify default data for a tool, maybe inside an xml? Alex ___ 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/
Re: [galaxy-user] default data for a tool
Hello Alex, Do you mean a default dataset (that a user can modify or never modify) or default form entry data? If default form entry data, then you can use the param tag set with value, as described in this wiki: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cparam.3E_tag_set Looking at existing tools that have default form data can provide good examples. For instance, the tool: galaxy-central / tools / filters / remove_beginning.xml See the content in param value=X / line 5 below 1 tool id=Remove beginning1 name=Remove beginning 2descriptionof a file/description 3command interpreter=perlremove_beginning.pl $input $num_lines $out_file1/command 4inputs 5 param name=num_lines size=5 type=integer value=1 label=Remove first help=lines/ 6 param format=txt name=input type=data label=from/ 7/inputs 8outputs 9 data format=input name=out_file1 metadata_source=input/ 10/outputs 12tests 13 test 14 param name=num_lines value=5/ 15 param name=input value=1.bed/ 16output name=out_file1 file=eq-removebeginning.dat/ 17 /test 18/tests 19help Hopefully this helps. If not, write back, or even better, add in some clarification and post a brand new question/thread to the galaxy-...@bx.psu.edu mailing list (the best list for development questions): http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Jen Galaxy team On 5/10/12 12:12 PM, alex wrote: Hi, Is there a way to specify default data for a tool, maybe inside an xml? Alex ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
[galaxy-user] Displaying bed files in ucsc
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/
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 jrobi...@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 won...@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/
