[galaxy-user] Question about extracting information from CEAS run results
I have run a ChIPseq work flow in galaxy, At teh end I ran CEAS: Enrichment on chromosome and annotation (version 1.0.0) to annotate the peaks which gave me a pdf file shoiwng distribution of peaks across genome with pie chart as well as well as histogram. It shows that ~5% of my peaks in 5UTR regions and other 3 % in 3' UTR 63 % exon and so on. Is there a way that I can have list of genes/ refrence ids which arein 5'UTR /3'UTR. I tried all tools in Galaxy but could not find it. There should be some way to extract these summarized results in details. Any one has a suggestion please? Thanks Kanwar ___ 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] long wait on jobs
Hi, I started a workflow yesterday (user name: antonymerlinj...@gmail.com) and it still hasn't gone past being queued to run. In fact, no jobs are running. Please advice. Thank you. Antony -- Antony M Jose, Dept. of Cell Biology Molecular Genetics, University of Maryland, Rm 2116, Bioscience Research Building, College Park, MD - 20742. ___ 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] Extract data and new genes
Hi Everyone, I am working with *Aedes aegypti * and I obtained around 500 million reads (HiSeq2000, 50bp). After doing all analysis of differential gene expression using known packages (Tophat, Cufflinks, Deseq etc) I was able to find a set of gene of interest, besides some functional group of genes that I already knew that I had to look at. Now, just looking over the 4,758 supercontigs and my data using IGV from Broad Institute (loading the genome and the SAM files from Tophat), I find a lot of potential new genes (hundreds or thousands of reads aligning to regions where there is no gene annotation), I also find new exons for some genes or exons with different sizes. I was thinking to do an *de novo* assembly to find new transcripts and genes, but I was wondering if there is something else I could do. For example, maybe I could just extract those regions where thousands of reads align (new gene). I know that we can extract the sequence data for specific transcript, is it possible to extract reads for regions without annotation, only based in the number of reads aligned? Maybe I could pull all the data together (from a couple sequencing lanes) and align it back to the genome, and then proceed to gene annotation. Another problem is that I am not sure how reliable would be the annotation only based on the data from HiSeq2000. I would appreciate if anyone one have some idea or suggestion in how to tackle this problem. Maybe *de novo* assembly is the way to go. Thank you. Luciano -- *Luciano Cosme* - PhD Candidate Texas AM Entomology Vector Biology Research Group www.lcosme.com 979 845 1885 co...@tamu.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/
[galaxy-user] Runtime on public Galaxy and current version of Galaxy on the Cloud?
Hi, I am finding that the run time on the public galaxy is exceptionally long, with job submitted yesterday still waiting to start. Given that I need to have analyses performed more quickly, I have tried to use Galaxy on the Cloud. Is this the following still the current version of cloudman to use? Current AMI: AMI: ami-da58aab3 Name: 861460482541/galaxy-cloudman-2011-03-22 I have set up instances for this version and have waited for over an hour for them to load, with multiple attempts to get the websites to open. All status indicators say that the instance is running. Any insight welcomed--- thanks--- Diana ** Diana Cox-Foster, Professor office: 536 ASI Bldg MAIL: 501 ASI Bldg Department of Entomology Penn State University University Park, PA, USA 16802 email: dx...@psu.edu office phone: 814-865-1022 dept. phone: 814-865-1895 ___ 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/
