[galaxy-user] upload problem
Hello, I am trying to upload 27.2 GB fastq file in Galaxy through FTP, but it throws an error: netout: Connection reset by peer 421 Service not available,remote server has closed connection. Please help. Thank you, Sujata ___ 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] Reference genome , fasta with or without gene feature
Dear All I am analysing bacterial RNA seq (illumina). as my reference genome is not in galaxy. so i need to downlaoded the reference genome from NCBI and upload to my history Should i use reference genome with gene features or single fasta file with out any annotation information. even after download should i need to modify or it should be used as it is. Thanks in advance Ateeq___ 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 Reference Genome
This explanations is very clear. Thank you – I was wondering about some of these issues as well. It would be wonderful if Galaxy could somehow make it possible to provide a bed file for the –G option or make it feasible to use GTF/bed output from the Table Browser tool as input to the –G option. (Maybe it already does?) GTF is an awkward format and BED would work just as well, if not better. Best wishes, Ann Loraine --- Ann Loraine, Ph.D. Associate Professor Department of Bioinformatics and Genomics University of North Carolina at Charlotte North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 alora...@uncc.edu http://www.transvar.org http://www.bioviz.org http://www.uncc.edu From: Jennifer Jackson j...@bx.psu.edumailto:j...@bx.psu.edu Date: Wed, 13 Jun 2012 16:12:27 -0700 To: Kristen Roop kristen.r...@gmail.commailto:kristen.r...@gmail.com Cc: galaxy-u...@bx.psu.edumailto:galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] Galaxy Reference Genome Hello Kristen, Our RNA-seq tutorial and FAQ can help out with the general workflow: https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq And an iGenomes reference annotation GTF dataset for mm9 is in the Shared Libraries here: (Import genes.gtf to your history, please ignore other content as it is under revision) http://usegalaxy.org - Shared Data - Data Libraries - iGenomes - mm9 To address your questions, one key misunderstanding may be the difference between a reference genome and a reference annotation dataset. * reference genome = genomic sequence (sourced in .fasta format) that the data is mapped against with TopHat and used as a scaffold for the RNA-seq tools. Since you are using mm9, selecting the built-in index for mm9 is an appropriate choice. A reference genome does not provide annotation beyond genomic positional coordinates. When using a mapping tool, including TopHat, there are mapping parameters that can be set to specify whether to keep only the best or all hits - it sounds as if you need to adjust these parameters in your run. The filter you ran (question #2) may have removed most or all hits - check the output from the SAM filter, was the output greatly reduced or empty? If so, re-run TopHat with parameters that keep the best hit from the start and move to Cufflinks from there without filtering through SAMTools. Help is on the tool form itself and in the links to the manual. * reference annotation = known transcripts (sourced in .gtf or .gff3 format) that are also mapped against the reference genome. These transcript annotations are the most useful when they contain gene, transcript start site, and other key attributes that the Cuff* tools can interpret. This annotation can guide assembly at various levels (loose or strict) depending on how the tool parameters are configured. The annotation MUST be mapped to the same exact reference genome that your FASTQ datasets are mapped to, with the same exact chromosome naming (see the RNA-seq FAQ for details). Help is also on the Cuff* tools including links to the manuals. More help, including links to tool help is on our wiki here: (see ' Tools on the Main server: Example: unexpected results with RNA-seq analysis tools.) http://wiki.g2.bx.psu.edu/Support#Interpreting_scientific_results Hopefully this helps, Jen Galaxy team On 6/13/12 7:07 AM, Kristen Roop wrote: Hello, Galaxy Main 1.) I am having trouble adding annotations to my Tophat and Cufflinks tools. I used the Mus.Musculus 9MM reference using the built in index. For the Tophat mapping but no annotations were available in the output files. I then tried converting the the Ref Genome from the UCSC to a SAM file using Sam Tools. Tophat would not recognize this but Cufflinks did. The Cufflinks output file did not have the annotation either. Any thoughts on the proper way to add annotations? 2.) I am also trying to filter the single mapped reads from the multiple mapped reads that resulted from Tophat. After converting the output file from Tophat I used the filter tool in the Sam Tools choosing 0x100 map is not primary. Afterwards I tried to run Cufflinks on the filtered output only to have it fail. My ultimate goal is to look at RNA seq gene expression. I know that I have to upload my files - groom using FASTQ groomer - download a reference sequence from UCSC - convert the reference genome file to a usable format -Run Tophat for mapping using the groomed file and the converted reference annotation - Filter the single mapped reads - Run cufflinks using the filtered single mapped reads from Tophat. From here I will continue with some other statistical analysis but right now I need to get this basic pipeline to work. Thanks, Kristen Roop ___ The Galaxy User list should be used for the
[galaxy-user] Page edition bug
Hi Galaxy team, I have two instances of galaxy on the same host, and have enabled page edition (I set enable_pages = True on universe_wsgi.ini file). I have set the parameter cookie_path different for each instance. I'm disconnected from galaxy when I try to edit a page content. But when I comment out the cookie_path for one instance it works for this instance. Did I miss something when configuring my instance ? Can someone give me some help ? I've tried to have a look at in the code but I'm not familiar with python. Thank you all, Felix Homa. ___ 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] FTP down?
Dear Sir or Madam, I have been attempting to upload a few datasets (2Gb) for the past few days but I cannot seem to login to the server. This has been the case since the server crashed last week. Could you please restart the ftp server? Many thanks, John -- John R. Clayton, PhD Université de Strasbourg Anopheles Group, CNRS UPR-9022 Réponse Immunitaire et Développement chez les Insectes Institut de Biologie Moléculaire et Cellulaire (IBMC) 15, rue René Descartes F-67084 CEDEX Strasbourg France Tel: +33 3.88.41.70.96 Fax: +33 3.88.60.69.22 Email: j.clay...@ibmc-cnrs.unistra.fr http://www-ibmc.u-strasbg.fr/ridi/index.php?cont_id=9lang=en ___ 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] FTP Error 530 Sorry, the maximum number of clients (3) for this user are already connected.
Hello, I have been unable to get a solid FTP connection to main.g2.bx.psu.edu for ~24hrs. Two things have occurred: 1) I get the error 530 Sorry, the maximum number of clients (3) for this user are already connected or 2) when finally connected, some files fail during transfer with 'incorrect password' while others continue uploading and eventually the entire connection is lost where attempts to reconnect give the 530 error in situation 1. To troubleshoot, I have tried all suggestions through FileZilla and Cyberduck, essentially limiting number of connections and disabling all before connecting, to no avail. It seems likely that this might be a server issue. Any insight is appreciated. ___ 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] generate pileup not working?
Hi, I am trying to do variants call with generate pileup. My steps where: 1. BWA 2. select only lines with the pattern Matching pattern: XT:A:U 3. SAM-to-BAM 4. then I tried to use Generate pileuphttps://main.g2.bx.psu.edu/tool_runner?tool_id=sam_pileupfrom BAM dataset However, it does not work, and I get the error message: 114: Generate pileup on data 97: converted pileup 0 bytes An error occurred running this job: *Samtools Version: 0.1.16 (r963:234) Error running Samtools pileup tool Floating point exception* Did I do anything wrong, or is it a bug? The parameters are copied below. Thanks, Lilach The parameters are: Tool: Generate pileup Name:Generate pileup on data 97: converted pileup Created:Jun 14, 2012 Filesize:0 bytes Dbkey:hg_g1k_v37 Format:tabular Tool Version: Tool Standard Output:stdouthttps://main.g2.bx.psu.edu/datasets/d038161e3fe9072e/stdout Tool Standard Error:stderrhttps://main.g2.bx.psu.edu/datasets/d038161e3fe9072e/stderr Input Parameter Value Conditional (refOrHistory) 0 Select the BAM file to generate the pileup file for 97: SAM-to-BAM on data 94: converted BAM Whether or not to print the mapping quality as the last column Do not print the mapping quality as the last column Whether or not to print only output pileup lines containing indels Print all lines Where to cap mapping quality 60 Conditional (c) 1 Theta parameter (error dependency coefficient) in the MAQ consensus calling model 0.85 Number of haplotypes in the sample 2 Expected fraction of differences between a pair of haplotypes 0.001 Phred probability of an indel in sequencing/prep 40 ___ 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/
