Re: [galaxy-user] Sequences are not currently available for the specified build.
Hi Rich, You could do this or you could switch to this version of the human genome (is in all of Galaxy's tools, but will not be useable at UCSC): Human (Homo sapiens) (b37): hg_g1k_v37 Thanks, Jen Galaxy team On 6/6/12 7:30 AM, Richard Linchangco wrote: Dear Jen, Thanks again! Does this mean I should upload a Custom Reference Genome? I have downloaded the genome specified by GATK for hg19. All I must do is upload to ftp, map it again, and then it should let me use it later on for Counting Covariates and the such? Sincerely, Rich On Wed, Jun 6, 2012 at 9:55 AM, Jennifer Jacksonj...@bx.psu.edu wrote: Hi Rich, Additional genomes will be specially sorted, indexed, and added to the GATK tool suite as it moves out of beta status. Hg19 is short-listed for addition near term. We do take requests to have genome added to tools and consider these when ranking our prioritization lists. Which genome did you want to use? One small warning when using a custom reference genome with this particular tool set - be sure to visit the GATK web site links directly to understand the sorting criteria for genomes. It can be different than how Galaxy, UCSC, and many of the existing tools already sort or instruct users to sort genomes or data. In short, the genome must be sorted in the exact order that it was originally released, but even this can be slightly confusing, especially if working with a non-human genome as there are few examples. Still, the documentation can help and tools are easily tested (if the sorting is wrong, the tool will fail and let you know). If others have requests for GATK native genomes, they are also welcome to reply. In general, key model organisms would be ranked highest in priority. We also try to get the largest genomes loaded natively first (for purely practical reasons). Good question, thanks! Jen Galaxy team On 6/5/12 8:01 AM, Richard Linchangco wrote: Dear Galaxy, I've been searching the lists for this type of issue and only found one solution thus far which is the use of a custom reference. It doesn't make sense in my situation because the reference I used was from Galaxy itself when I mapped my data. I'm now trying to use GATK to find SNPs but no matter what I've tried I can't get past this issue. I'm trying to use the Count Covariates and the Unified Genotyper but to no avail. The only issue appears to be that Sequences are not currently available for the specified build. Any help would be much appreciated. Thanks Sincerely, Rich -- Jennifer Jackson http://galaxyproject.org -- 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] Sequences are not currently available for the specified build.
Dear Galaxy, I've been searching the lists for this type of issue and only found one solution thus far which is the use of a custom reference. It doesn't make sense in my situation because the reference I used was from Galaxy itself when I mapped my data. I'm now trying to use GATK to find SNPs but no matter what I've tried I can't get past this issue. I'm trying to use the Count Covariates and the Unified Genotyper but to no avail. The only issue appears to be that Sequences are not currently available for the specified build. Any help would be much appreciated. Thanks Sincerely, Rich -- Richard Linchangco PSM in Bioinformatics College of Computing and Informatics University of North Carolina at Charlotte Tel: (630)440-7010 rlinc...@uncc.edu, rlin...@gmail.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/
Re: [galaxy-user] Sequences are not currently available for the specified build
Hello Mark, Not all genomes in the database assignment list are pre-index for all tools. That is the case for this genome. We can consider add this in, but it would actually be quicker for you to simply load a fasta version of the genome into your history and use it as a custom reference genome from there. Most tools have some variation of the choice on the SAM-BAM tool form's option: Choose the source for the reference list: set as History. Load the genome using FTP, as explained here: http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP Best wishes for your project, Jen Galaxy team On 10/24/11 7:46 AM, Mark Silby wrote: Hi all, We are just beginning to analyze RNA-seq data and hope to make use of the Galaxy tools. We are not using a commonly studied organism such as human. Rather, our data are from the bacterium Pseudomonas fluorescens Pf0-1. The genome for P. fluorescens Pf0-1 appears in the database/build menu, and we have selected this in the .sam file attributes. When we run the sam to bam conversion, we get the error Sequences are not currently available for the specified build. Is this something that can be corrected easily? Many thanks for your help. Mark Silby ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
