[galaxy-user] a question about cuffdiff values
Hello: I am a Galaxy-naive molecular, developmental biologist studying repression/derepression of early embryonic gene expression in zebrafish embryos. After attending the Galaxy meeting I returned home and worked up two mRNAseq files to determine RNA expression differences using cuffdiff between a treated and an untreated sample (i.e. data from cuffdiff under the title of gene differential expression testing). I downloaded the data, opened it up in an Excel file and captured all the significant rows. If I look at the value 1 and value 2 columns I find that many of the numbers are single digits. I expect that in one of the columns that the numbers will be very low (that is, less than 1) because the treatment should be inducing gene expression in a subfamily of genes that are repressed. My questions are: 1) what do these numbers represent? 2) If in the value column where I expect a higher number has a value of 10 or less mean anything or should one be selecting for values higher that these single digit numbers 3) And in the column of genes that might be repressed is there really a difference between a value of 0.1 versus something like 0.01 since that can change my log ratios significantly--this, of course, goes back to my first question I would appreciate any help I could get, sincerely, el linney Professor of Molecular Genetics and Microbiology Duke University Medical Center ___ 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] gene names from cuffdiff data
How does one get gene names when using cuffdiff when looking at gene differential expression testing results? I am doing some +/- exposure studies with zebrafish embryos and then processing the 50bp single-ended fastq files through Galaxy with particular interest in the cuffdiff readout of differential gene expression. It seems to be working well but my readout is only giving me gene ID's. It would by more efficient if I could get gene names from the output. I suspect I may be able to do this through selection of options from the UCSC TABLE BROWSER when I use its Zv9 danRer7 assembly as a reference genome. I see a place for selected genes but not for all the identified genes. Is this something that could be done directly or is there just a beyond Galaxy method of gene gene lists from a list of gene ID's. Thanks, el linney Duke University Medical Center ___ 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] does Galaxy have a tool for converting .sra files to fastq files?
Hello, I would like to download some GEO files that complement my own research with zebrafish embryos but apparently GEO is now only providing .sra flles. For a not very experienced unix person, does Galaxy have a tool for this or is there a clear description somewhere else of how to do it for someone who is not a bioinformaticist? Thanks, el linney Duke University Medical Center ___ 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] downloading problems from main Galaxy
Problem: when downloading steps in histories back to my computer the files are sometimes incomplete (by incomplete I mean a significantly smaller size that given during the download indicator) Description: after processing RNAseq files on main Galaxy I have the memory to download steps or complete histories; this past week I have noticed, in a random way that some individual tophat alignments or cuffdiff analyses do not download completely to my computer--sometimes they do, but its random right now Questions: Is there something I can do to eliminate this? Does this have anything to do with how busy Galaxy is? I notice that it sometimes happens even if I try to download one file at a time el linney Duke University Medical Center ___ 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] cannot download data to Galaxy
Hello, My connection with Galaxy online shutoff last night while I was transferring data to it. When I tried to connect again with Fetch this morning I was not allowed and a message like Sorry the maximum number of clients for this user are already connected. I have had what appears to be the bad habit of not logging off to Galaxy. I am working on the same data sets with three different computers, I only have one login to Galaxy, so yes, I was logged in on 3 different computers. When I logged off of them, and tried to transfer data, I still got the same message. I realize people might be trying to get around the 250gb limit by having multiple logins--I am not one of them, I am the only user on the three computers I am using. If not logging off when I leave the computer is a problem to Galaxy, I will religiously log off each time I am not using the computer (the computers are in three different rooms in my lab and my lab consists of just me and a tech--I am the only one who knows the computer login for both the computers and for Galaxy). If I have created a problem by being lazy, I apologize, but I have grown dependent upon using Galaxy online and some new data just came in. Sincerely, Elwood Linney Professor of Molecular Genetics and Microbiology Duke University Medical Center ___ 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] portal to galaxy restricted
A message sent earlier this week by me indicated that I could not connect to Galaxy via Fetch to download data. A reply indicated a glitch was fixed. I then could connect with Fetch and I tried to transfer 4 x 16gb files and the connection disconnected about 4 times. Now, once again, I cannot connect with Galaxy online to transfer data. Is this a problem that can be solved-either at my end or at Galaxy? Elwood Linney ___ 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] estimating galaxy on the cloud needs for RNAseq
Questions: I have been running sets of data for cufflinks/cuffdiff analysis on Galaxy online--I am considering using the cloud but from what I can read, because of different person's galaxy needs, I can't get an clear idea of what I would need and how long it would take to process (and the cost) if I am running weekly 4 x 16gb fastq files to 6-8 x 16gb files--one set per week Is anyone out there using the cloud exclusively for this type of analysis? And can you give me an idea of what type of cloud setup I could use? I have no idea of how much time it would take to process these on the cloud so its hard to estimate setup costs and specific requirements. Elwood Linney ___ 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] Online galaxy turning everything red on RNAseq steps
Hello, I have been waiting a few weeks to process some RNA seq datasets but woke up this morning with lots of steps red. I thought it just might be because of the movement of the system but I processed steps for some histories and everything has turned red. I also noticed that online Galaxy now has RNAseq steps separated into two sections--does this have something to do with the problems? el linney Duke University Medical Center ___ 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] problems in transitioning from Tophat to Cuffdiff
After successfully using RNAseq software in Galaxy online for about 10 different datasets to just get gene expression differences between replicates from control versus exposed zebrafish embryos, I am having no luck getting cuffdiff to work with the moved Galaxy. I had this problem with histories developed before the move and histories developed after the move. I have had this problem using an order cuffmerge gtf file that worked in the past in Cuffdiff, with a new cuffmerge file developed from cufflinks of the files and by just using a ref file gtf from UCSC. I don't know if this is just some interface problem with a different version of the software that was included with the move, or a reference genome that does not interface with Cuffdiff. It has happened with about 5 different histories. Is anyone else having this problem? And found a solution? Elwood Linney ___ 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] Same RNAseq samples give different FPKM values when run against different samples
Hello, I am sure this has come up before and maybe I missed the answer. If in using cuffdiff I run a sample 1(3 repeats) vs a sample 2 and then run the same sample 1(3 repeats) against a sample 3 or a sample 4, I get different value for fpkm from sample 1 each time. Is there something going wrong here or is there something in the program that causes this difference? I have seen this with online Galaxy and with the instance I have on my Mac Pro el linney Duke University ___ 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] adding danrer7 as a reference genome for tophat2
Can you add danrer7 as a reference genome for tophat2 for online Galaxy? Its there for tophat for Illumina. Elwood Linney ___ 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/
