[galaxy-user] problem with cuffdiff
Hy guys, I am performing some RNA sequencing. I am using a gtf file as a reference annotation for the cufflink - cuffmerge steps. Then when I do the cuffdiff I find something strange. Where there is the gene name, the corresponding values (all of them!) are 0, where there is no gene name there are values of expression, fold change etc. Does anyone have an idea of what is going on? I haven't find any similar question in the Galaxy archive. Also, I tried to visualize my outputs (TopHat Cufflink Cuffmerge) using Trackster but it gives me an error. Is anyone experiencing the same problem? Thanks, Giuseppe ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] (no subject)
Hi, I have worked so far on the free web-based version of Galaxy; now I have installed Bio-Linux 7, and there is Galaxy in there as well. However, I cannot access to my data (stored on the web version of Galaxy) using Galaxy on Bio Linux. If it is possible, does anyone know how to do it? Thanks, Giuseppe Ianiri ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] software post alignment
Hello, I performed my mapping using tophat - cufflink - cuffmerge - cuffdiff. With the information I have for my analysis so far, I can reannotate wrong genes, check for correct splicing etc. However, I would like to perform some analysis post-alignment, like for example samples clustering, volcano plot, heat maps etc. I guess I can't do this kind of analysis with Galaxy (I am using the free version on line on my Windows laptop) since I haven't found anything in the tools section. Does anyone know a software that I could use in windows with the data obtained in Galaxy? Any suggestion is really appreciated. Regards, Giuseppe Giuseppe Ianiri, Ph.D. Division of Cell Biology and Biophysics School of Biological Sciences 5100 Rockhill Road University of Missouri-Kansas City Kansas City, MO 64110 Email: iani...@umkc.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] filter for +/- 2-fold difference in expression levels
Hey guys, I have my Cuffdiff output and I was trying to figure out how to get the data I need. I am interested in the outputs Transcript and Gene differential expressed. Does anyone know how to filter for +/- 2-fold difference in expression levels? Thank you Giuseppe Ianiri, Ph.D. Division of Cell Biology and Biophysics School of Biological Sciences 5100 Rockhill Road University of Missouri-Kansas City Kansas City, MO 64110 Email: iani...@umkc.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] filter for +/- 2-fold difference in expression levels
Thank you Jennifer. I just start working with these things, so I am wondering which minimal value of FPKM I should use in the filter tool. Do you have an advice or an example that I could look at? Thank you Giuseppe Ianiri, Ph.D. Division of Cell Biology and Biophysics From: Jennifer Jackson [j...@bx.psu.edu] Sent: Thursday, November 29, 2012 10:51 AM To: Ianiri, Giuseppe Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] filter for +/- 2-fold difference in expression levels Hello Giuseppe, Fold is included in the Cuffdiff output. Section Differential expression tests, first file, column #9. http://cufflinks.cbcb.umd.edu/manual.html A tool like Filter and Sort - Filter could be used to subset specific values. Hopefully this helps, Jen Galaxy team On 11/29/12 5:35 AM, Ianiri, Giuseppe wrote: Hey guys, I have my Cuffdiff output and I was trying to figure out how to get the data I need. I am interested in the outputs Transcript and Gene differential expressed. Does anyone know how to filter for +/- 2-fold difference in expression levels? Thank you Giuseppe Ianiri, Ph.D. Division of Cell Biology and Biophysics School of Biological Sciences 5100 Rockhill Road University of Missouri-Kansas City Kansas City, MO 64110 Email: iani...@umkc.edumailto:iani...@umkc.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] Cuffdiff without gene annotation
Hello guys, I went through the RNAseq workflow (I didn't do Cuffmerge) and from the Cuffdiff output gene and transcript differential expression testing I filtered some data. For example, for two samples I got about 400 gene and 900 transcript differential expressed with fold change 2. Since I am working with a fungus whose genome annotation is in a format (gff) not accepted by Cuffmerge or Cuffcompare in Galaxy (the accepted one is GTF2), the Cuffdiff output tells me only the position of relevant genes on the scaffolds. Going to genome browser and see which gene is in that position is fine for few genes, but doing that for all 400 or 900 is something probably impossible. Does anybody have a helpful suggestion on what I can do? It would be great if there was a program where based on the position of the genes on the scaffold (Cuffdiff output) I can get their information using the annotation file. I have also the gene annotation file in gene bank format (gbk) but I don't see a way to use it for what I need. Thanks Giuseppe Ianiri, Ph.D. Division of Cell Biology and Biophysics School of Biological Sciences 5100 Rockhill Road University of Missouri-Kansas City Kansas City, MO 64110 Email: iani...@umkc.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/
