[galaxy-user] Cannot get rid of custom build error
Hello, I've tried to create a custom build (starting from the trackster page) and clearly made some mistake. I get a NoConverterException error which is almost certainly my fault putting something wrong in. However, now the Custom Builds page shows this error and I cannot make it go away. I have a local install, have killed and restarted, logged in and out, but still this error stays. I cannot try to enter another custom build because there is nothing on the page except this error. Does anyone kow how to get rid of this? Any help in getting around this error are appreciated. Jim ___ 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] fastq groomer
Hello Slon, In case you are still having issues, the best use case for Illumina 1.8+ data is to run the FASTQ Groomer tool with the option Sanger. As Peter noted, this assigns the expected datatype plus verifies content before investing time in downstream analysis. Please let us know if more help is needed, Best, Jen Galaxy team On 10/18/11 1:02 AM, arabidopsis wrote: Hi all, Fastq groomer has Solexa or Illumina 1.3+ as an input quality format. I asked at the sequencing facility about their machine and output and they said their format was Illumina 1.8+ (the newest). I tried to convert my fastq file into Sanger by fastq groomer, using Illumina 1.3+ as an input option and got all reads with quality of around 10... Does it mean that Galaxy cannot be used on a dataset with 1.8+ encoding or something else was wrong? Thanks, Slon ___ 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/
Re: [galaxy-user] Names for genes in RNA-Seq analysis
Hello Michael, The UCSC RefSeq Genes track's has the data: 1) a transcript accession, in column name 2) a gene symbol, in column name2 but not from the Table Browser's GTF format output, as explained at: http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format Ensembl is another data source choice for full functionality, at it contains: transcript_id, gene_id, and gene_name. This help from the tool authors is also worth reviewing: http://cufflinks.cbcb.umd.edu/gff.html Note that specific questions about these tools can also be directed at: tophat.cuffli...@gmail.com Hopefully this helps, Jen Galaxy team On 10/26/11 9:24 AM, Michael Gooch wrote: Regarding the GTF files for cuffllinks, how do I obtain one for all human mRNA that actualy contains gene names rather than accession numbers. I went to the UCSC table browser but their files contain accession numbers that I dont know how to decode en-masse. ___ 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/
Re: [galaxy-user] get data through FTP site
Hello, Would one or both of you have time to try this again? If the transfer from the FTP area to a history fails (or is incomplete) again, please let us know and we can examine. If the Galaxy account you are using is linked to a different email, please note that in the reply. Thanks for the help, Jen Galaxy team On 10/27/11 7:55 PM, LOURO Bruno wrote: Hi, I faced a similar problem with getting data into history, I tried directly and via FTP. Both cases, the files being loaded to history ended up being incompleted. The upload to FTP was OK. My files were .bzip2. Cheers, Bruno De: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] Em Nome De Jennifer Jackson [j...@bx.psu.edu] Enviado: quinta-feira, 27 de Outubro de 2011 21:23 Para: Benoit HENNUY Cc: galaxy-u...@bx.psu.edu Assunto: Re: [galaxy-user] get data through FTP site Hello, Please try an alternate name/compression format. The de tails for supported file names (no spaces) and compression types (.gzip, .bz, bzip2, and single-file .zip) are here: http://galaxyproject.org/Learn/Upload%20via%20FTP Please let us know if we can help again, Best, Jen Galaxy team On 10/26/11 6:25 AM, Benoit HENNUY wrote: Hello, I uploaded (on Oct, 25) data through FTP site and I was not able to retreiven them to include them in a history. I suppose that the files should appeared in the FTP list under the Get data page. THese data are named P2 fastq .gz files that I wold like to use in RNA Seq workflow. Thank you to help me to be able to use these data. Best regards, Benoit HENNUY GIGA Genomics University of Liege Belgium ___ 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/ -- 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/
Re: [galaxy-user] Genome database/builds missing?
Hello Dan, Are you still seeing this issue? At the Main Galaxy location http://usegalaxy.org (http://main.g2.bx.psu.edu)? If yes, please share a link to your history (to me directly), and note the datasets that are presenting this problem and the exact tool/steps you are using to assign database. Best, Jen Galaxy team On 10/26/11 10:25 AM, Daniel N. Hupalo wrote: I've been using galaxy to analyze maf files and today the drop down list for database/builds for genomes has lost most of the genomes once listed. I no longer see any bacteria or plants on the list, specifically TAIR9 arabidopsis is no longer on the drop down list when it was just yesterday. Did something change? Thanks - Dan ___ 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/
Re: [galaxy-user] Names for genes in RNA-Seq analysis
Dear Jennifer Actually the problem was coming from a non usable Ensembl GTF file. I used the workflow in http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq And remade the Cufflink analysis using the new GTF file as a reference and, BINGO, it worked. Thank's for your help Best Olivier Le 28/10/11 20:19, « Jennifer Jackson » j...@bx.psu.edu a écrit : Hello Olivier, When deleting data, it takes the server a short amount of time to refresh. It may take a bit longer right now since many people are performing this action at the same time. For the RNA-seq analysis question, reference annotation GTF files are used by the Cuff* programs. (These are different than the result GTF files produced by the programs). For reference annotation GTF files, there are many sources, including Ensembl and UCSC. Here are links to a tutorial and an FAQ that can help with your usage question. http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq But, there are many small details to running the tools to get the optimal results. These types of questions concerning functionality are best directed to the tool authors at tophat.cuffli...@gmail.com Take care, Jen Galaxy team On 10/25/11 11:24 PM, GANDRILLON OLIVIER wrote: Hello Jennifer Le 26/10/11 02:15, « Jennifer Jackson »j...@bx.psu.edu a écrit : Hello Olivier, Are you using a reference gene annotation GTF file? Well if I do , I do not know :-) What I used is first TopHat and then Cufflink. At what stage shall I use such a GTF file? And additionnaly: where shall I find such a GTF file? As I understand it: there are tow sources for a GTF file: 1. The output from cufflinks generates one (but there is no gene names in it..) 2. I could get one from Ensembl? Shall I then use Cuffcompare on the cufflink output? Best Olivier PS: I am now stuck with the galaxy websute that state that I am over my disk quota. I have deleted a couple of files but this does not seems to help... -- 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/
[galaxy-user] Expected Transcriptome BLAST
Hey, Jack Colicchio here, a PhD. student at KU. I am about to get an illumina Next gen transcriptome data setthat I would like to align and quantify against a list of expected transcripts from Mimulus guttatus. The expected transcripts are in .gff format, and I was wondering how I could get that file uploaded to you're website to allow me to align my transcriptome against. I successfully uploaded the .GFF file, and can view it on your site, but do not know how I could blast my .fastq data from illumine against this file. Thanks, Jack ___ 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] Removing low quality reads
Hi Getiria, Galaxy does not have a tool to do this directly (but it would be a nice addition). Converting to SAM and using a combinations of tools in Text Manipulation would likely be possible. It would involve several steps and some experimentation, but a workflow could be created from that result to do the filter at all once in the future. Sorry that we could not help more, Best, Jen Galaxy team On 10/24/11 9:15 AM, Getiria Onsongo wrote: Galaxy Users, I would like to filter a .bam file to remove reads with low mapping quality, especially ambiguously mapped reads (MAPQ = 0). I can easily do this using the command line version of samtools as shown below. samtools view -bq 20 hba1.bam hba1_MAPQ20.bam None of the options available under NGS:SAM Tools (e.g., Generate pileup and Filter SAM) provide an option for removing reads with low mapping quality. The history shown in http://main.g2.bx.psu.edu/u/onsongo/h/obtaininghighqualityreads shows the results I would like to obtain. Data 2 shows the results of Picard tools SAM/BAM Alignment Summary Metrics http://main.g2.bx.psu.edu/tool_runner?tool_id=PicardASMetrics on hba1.bam which contains reads with MAPQ values less than 20. As shown in this summary html, PF_READS_ALIGNED = 775 and PF_HQ_ALIGNED_READS = 241. Data 4 shows the results of Picard tools SAM/BAM Alignment Summary Metrics http://main.g2.bx.psu.edu/tool_runner?tool_id=PicardASMetrics on hba1_MAPQ20.bam which contains only reads with MAPQ greater than or equal to 20. As shown in this summary html, PF_READS_ALIGNED = 241 and PF_HQ_ALIGNED_READS = 241. Is there a way in Galaxy to filter a bam file to remove low quality mapped reads similar to using the samtools command line alternative shown above? Thanks, Getiria -- Getiria Onsongo, Ph.D. Bioinformatics Research Scientist Masonic Cancer Center, University of Minnesota Minneapolis, MN 55455 Phone: 612-625-0101 tel:612-625-0101 ___ 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/
Re: [galaxy-user] Galaxy tracker browser freezes when zoomed in
Hi Steve, This means that the Visualization tool is calculating an index. It should eventually finish or you can choose another view (dense or histogram). That said, this tool is under active development, and if you would like to share a link to the visualization, we can take a look to see if this is a known or not. Best, Jen Galaxy team On 11/2/11 9:07 AM, Steve wrote: Hi, I'm going through the RNA-seq exercise at http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise. I'm at step 2 of mapping the reads where I've run tophat and have loaded the output files and the regGene tracks onto a new track browser. When I zoom in (to ~45kbp window), the accepted hits and one of the splice junction tracks from tophat do not show data and instead show a crossed pattern and the browser no longer allows clicking and dragging to move the window. Please advise. Cheers, Steve ___ 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/
Re: [galaxy-user] Expected Transcriptome BLAST
Hello, To use a custom genome with the alignment tools at Galaxy Main (http://usegalaxy.org), the dataset must be in fasta format. If the data is RNA, then using the tools in NGS: RNA Analysis will accept both a reference custom genome and a transcript file in GTF format to guide placement (using TopHat as the preferred alignment tool). It is important to note that the Main Galaxy site does not offer a BLAST option (with the exception of Megablast against a specific set of genomes), but a local or cloud instance would, using the BLAST tools in the tool shed and setting up your own data. Some help links: If using the RNA Analysis tools at Galaxy Main: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP If using a local or cloud instance: http://getgalaxy.org http://galaxyproject.org/wiki/Admin/Cloud http://galaxyproject.org/wiki/Tool%20Shed Hopefully this offers you a choice that will work for your project, Best, Jen Galaxy team On 11/2/11 10:03 AM, Colicchio, Jack M wrote: Hey, Jack Colicchio here, a PhD. student at KU. I am about to get an illumina Next gen transcriptome data setthat I would like to align and quantify against a list of expected transcripts from Mimulus guttatus. The expected transcripts are in .gff format, and I was wondering how I could get that file uploaded to you're website to allow me to align my transcriptome against. I successfully uploaded the .GFF file, and can view it on your site, but do not know how I could blast my .fastq data from illumine against this file. Thanks, Jack ___ 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/
Re: [galaxy-user] Dataset not appearing as available input to SAM analyses
Hi Clare, Galaxy is fairly transparent, so this occurs sometimes and can mean that either the server is very busy or there is another problem, perhaps with the dataset. Please note that mpileup is not supported yet, just pileup, although this is on our short list of to-do upgrades. If you used mpileup, this could very likely be the root cause of the tool error (server error). You can track the upgrade to mpileup through this ticket: https://bitbucket.org/galaxy/galaxy-central/issue/524 To troubleshoot a pileup file: 1 - double check the format of your data again the specification as outlined on the tool form for NGS: SAM Tools - Generate pileup from BAM dataset. 2 - try running the file type assignment again the job again to double check against a transient error. If pileup was used and the cause of the error is still unclear, we take a look we can provide feedback. Please share a link to your history using Options - Share or Publish from the top of the history panel, generate a share link, then email that back to me directly. Please note which dataset presents the problem and confirm that samtools pileup was used. Thanks! Jen Galaxy team On 11/2/11 8:12 AM, James Nelson wrote: Thanks Jen, but the very first time I tried changing the type to pileup, Galaxy came back with Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) I somehow don't think the user's supposed to see the error logs or exception reports, so what next? Clare - Original Message - From: Jennifer Jacksonj...@bx.psu.edu To: James Nelsonj...@k-state.edu Cc: galaxy-u...@bx.psu.edu Sent: Wednesday, November 2, 2011 8:11:09 AM Subject: Re: [galaxy-user] Dataset not appearing as available input to SAM analyses Hello Clare, Perhaps the loaded pileup datasets are not assigned to the pileup datatype? Click on the pencil icon in the right upper corner of the loaded pileup dataset, then use Edit Attributes - Change data type. Hopefully this helps, Best, Jen Galaxy team On 10/29/11 4:10 PM, James Nelson wrote: Hi, I'm trying to use the SAM/Filter pileup analysis on some pileup output files I've uploaded. But when I click the analysis link, these output files don't appear in the Select dataset dropdown menu; instead only one file, the output from FASTQ Summary Statistics which is obviously not pileup output, is shown. Thanks Clare Nelson ___ 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/
Re: [galaxy-user] Downloading files
Hi Marc, Datasets can be downloaded over the command line by using e.g. wget or curl; right click the disk icon that you would ordinarily use for saving and copy the link location and paste that into your command line, something like: wget 'http://test.g2.bx.psu.edu/datasets/a4bee4ca343f03ba/display?to_ext=fasta' The team is working no other strategies to enable the download of large histories/datasets but nothing is in place yet. Hopefully this helps, Jen Galaxy team On 10/30/11 12:36 PM, KNIGHT M.R. wrote: Is there any way of downloading processed files by e.g. FTP, rather than “Save as” in the web browser? I have a large (9.6Gb) BAM file to download, and downloading it via the browser seems unstable for some reason. Thanks, Marc. ___ 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/
Re: [galaxy-user] Expected Transcriptome BLAST
Also, I'm working under John Kelly and Lena Hileman at KU. We, along with our collaborators at Duke, would get a lot of use out of an expected transcriptome that we could blast illumine data against. If we sent you our genome in .fasta format along with the .gff expected transcript file is their anyway you could combine these into a database we could align against? -Jack On Nov 2, 2011, at 12:03 PM, Jack Colicchio wrote: Hey, Jack Colicchio here, a PhD. student at KU. I am about to get an illumina Next gen transcriptome data setthat I would like to align and quantify against a list of expected transcripts from Mimulus guttatus. The expected transcripts are in .gff format, and I was wondering how I could get that file uploaded to you're website to allow me to align my transcriptome against. I successfully uploaded the .GFF file, and can view it on your site, but do not know how I could blast my .fastq data from illumine against this file. Thanks, Jack ___ 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/
