[galaxy-user] Illumina Methylation tool in toolshed
Hi, This is my third post regarding this matter but however I didn't get any reply. I am trying to find a tool for r Illumina Methylation. Is there any available on the tool shed or test tool shed? Thanks, Sachit ___ 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/
Re: [galaxy-user] Illumina Methylation tool in toolshed
Hi Sachit, not in the toolshed but you can find a start here: https://github.com/bgruening/galaxytools/tree/master/illumina_methylation_analyser its for the 450k chips, I have also some tools for WGMA if you are interested. Cheers, Bjoern Hi, This is my third post regarding this matter but however I didn't get any reply. I am trying to find a tool for r Illumina Methylation. Is there any available on the tool shed or test tool shed? Thanks, Sachit ___ 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/
Re: [galaxy-user] Illumina Methylation tool in toolshed
Hi Bjoern, Thank you for your reply. To be precise I am looking for a wrapper of * lumi. *http://www.bioconductor.org/packages/2.12/bioc/html/lumi.html Do we have that in main tool shed or test tool shed or in github? Thanks, Sachit On Mon, Jul 29, 2013 at 2:53 PM, Bjoern Gruening bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Sachit, not in the toolshed but you can find a start here: https://github.com/bgruening/galaxytools/tree/master/illumina_methylation_analyser its for the 450k chips, I have also some tools for WGMA if you are interested. Cheers, Bjoern Hi, This is my third post regarding this matter but however I didn't get any reply. I am trying to find a tool for r Illumina Methylation. Is there any available on the tool shed or test tool shed? Thanks, Sachit ___ 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/
Re: [galaxy-user] Illumina Methylation tool in toolshed
Not that I know of, mine is wrapping IMA. cheers, Bjoern Hi Bjoern, Thank you for your reply. To be precise I am looking for a wrapper of * lumi. *http://www.bioconductor.org/packages/2.12/bioc/html/lumi.html Do we have that in main tool shed or test tool shed or in github? Thanks, Sachit On Mon, Jul 29, 2013 at 2:53 PM, Bjoern Gruening bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Sachit, not in the toolshed but you can find a start here: https://github.com/bgruening/galaxytools/tree/master/illumina_methylation_analyser its for the 450k chips, I have also some tools for WGMA if you are interested. Cheers, Bjoern Hi, This is my third post regarding this matter but however I didn't get any reply. I am trying to find a tool for r Illumina Methylation. Is there any available on the tool shed or test tool shed? Thanks, Sachit ___ 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] Filter fastq by percentage of ambiguous (N) bases
Hello, I like to filter my fastq files (50 bp single end Illumina RNA seq reads) by a maximum threshold (10%) of ambiguous (N) bases. I can see that the CLIP tool removes all reads with one or more N bases. Is there a way to remove only the reads with five or more N bases using Galaxy? Thank you. Best wishes, Anto ___ 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] Problem with SAM-to-BAM conversion
Hello, I am trying to map Illumina paired-ends reads from the nematode Caenorhabditis briggsae. Here are the steps of my history: 1)I uploaded and groomed two .fq files corresponding to paired-end reads. In the attributes, I choose the cb4 database. 2)I mapped them using BWA (BWA Version: 0.5.9-r16 BWA run on paired-end data). However, I used the cb3 database here, since the cb4 was not available. 3)I filtered the output SAM file for mapped reads (galaxy tool version 1.0.0). cb3 is still said to be the reference database in the filtered SAM I got as output. 4) Then I tried to convert the SAM into BAM. Here it failed. When I chose the parameters of this tool, what I had for the 1st option Choose the source for the reference list is either: -from the history -locally cached I chose locally cached. Then, when running the tool, and I had this message error: 20: SAM-to-BAM on data 16: converted BAM error An error occurred with this dataset: Samtools Version: 0.1.18 (r982:295) No sequences are available for build (cb3), request them by reporting this error. As recommended, I report you now this error ! I found a similar problem in the Galaxy_user mailing list... But I did not get how the problem was solved ! http://user.list.galaxyproject.org/SAM-to-BAM-conversion-problem-td4135498.html I tried to change the attributes of the SAM and filtered-SAM files to cb4, but it did not work. Note also that in the error report, the version is said to be 0.1.18. But when I click on the SAM-to-BAM tool, the header of the page says: SAM-to-BAM (version 1.1.2). I don't know if this matters or not. Could you please help me fixing this issue ? Many thanks ! -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesn...@biologie.ens.fr Tel: +33-1-44-32-39-44 ___ 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/
Re: [galaxy-user] Problem with SAM-to-BAM conversion
Hi Fabrice, I work on C. elegans too, and I have found that you need to have the same ce genome database for all steps; otherwise, some tools won't work later in your workflow. With some help from the Galaxy staff, I discovered that there is a version of ce10 in the CloudMap shared information on the Galaxy server. You can find it under CloudMap ot266 proof of principle dataset. I found it works well to copy this file into your history. When I used GATK tools, it requests the location of your genome datafile: locally cached versus history. If you choose history, it always finds the ce10 version that you put there. Not sure this will help with SAM to BAM conversion, but ce10 is a more up to date version of the database anyway. And the CloudMap version is sorted in a way that is GATK-friendly, which was necessary for my application. Hope this helps, Sam Politz -Original Message- From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Fabrice BESNARD Sent: Monday, July 29, 2013 9:58 AM To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] Problem with SAM-to-BAM conversion Hello, I am trying to map Illumina paired-ends reads from the nematode Caenorhabditis briggsae. Here are the steps of my history: 1)I uploaded and groomed two .fq files corresponding to paired-end reads. In the attributes, I choose the cb4 database. 2)I mapped them using BWA (BWA Version: 0.5.9-r16 BWA run on paired-end data). However, I used the cb3 database here, since the cb4 was not available. 3)I filtered the output SAM file for mapped reads (galaxy tool version 1.0.0). cb3 is still said to be the reference database in the filtered SAM I got as output. 4) Then I tried to convert the SAM into BAM. Here it failed. When I chose the parameters of this tool, what I had for the 1st option Choose the source for the reference list is either: -from the history -locally cached I chose locally cached. Then, when running the tool, and I had this message error: 20: SAM-to-BAM on data 16: converted BAM error An error occurred with this dataset: Samtools Version: 0.1.18 (r982:295) No sequences are available for build (cb3), request them by reporting this error. As recommended, I report you now this error ! I found a similar problem in the Galaxy_user mailing list... But I did not get how the problem was solved ! http://user.list.galaxyproject.org/SAM-to-BAM-conversion-problem-td4135498.html I tried to change the attributes of the SAM and filtered-SAM files to cb4, but it did not work. Note also that in the error report, the version is said to be 0.1.18. But when I click on the SAM-to-BAM tool, the header of the page says: SAM-to-BAM (version 1.1.2). I don't know if this matters or not. Could you please help me fixing this issue ? Many thanks ! -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesn...@biologie.ens.fr Tel: +33-1-44-32-39-44 ___ 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/ ___ 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] Problem with ftp connexion to Galaxy
Hello, I registered some time ago to Galaxy. From the very beginning, my ftp connexion is not working. I am using Filezilla, on a windows operating system. More precisely, the connexion can be established, but the process fail when it is asking for the password. Statut :Résolution de l'adresse de main.g2.bx.psu.edu Statut :Connexion à 128.118.250.4:21... Statut :Connexion établie, attente du message d'accueil... Réponse : 220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP) [:::128.118.250.4] Commande : USER fbesn...@biologie.ens.fr Réponse : 331 Password required for fbesn...@biologie.ens.fr Commande : PASS *** Réponse : 530 Login incorrect. Erreur :Erreur critique Erreur :Impossible d'établir une connexion au serveur I sent an email two month ago to report this problem. I was answered that this was an issue happening with the new accounts created. Obviously, this issue has not been fixed yet, has it? If yes, could you indicate me to make my ftp connexion works now ? Thank you for your help !! -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesn...@biologie.ens.fr Tel: +33-1-44-32-39-44 ___ 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] SNPeff
Hello, I would like to use SNPeff for annotation through GATK, However when I upload my file it seems like I cannot use it for this task. My file is .txt and is in this format : Chr locationref allele alt allele 1 1234567A T/C What am I doing wrong? Thanks, Andréanne ___ 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] Cuffdiff-cummerbund with biological replicates problem
I'm trying to run Cuffdiff on a set of 10 human samples with biological replication then download the results for further analyses in Cummerbund(v2.1.1). It seems like a standard workflow but I cannot get cummerbund to acknowledge replicates. I download and rename the 11 cuffdiff output files to the names expected by cummerbund. Cummerbund builds a CuffSet with no warnings and most analyses work as expected. The problem comes any time I try to see the results of replication. For example, in cummerbund, replicates() returns an empty set and any type of plot returns an error when replicates=T is included as an argument. There is no evidence of replication data in any of the 11 cuffdiff output files. The data is presented with the group name only. From this, I conclude that the problem is with cuffdiff, since there is no replicate data for cummerbund to build into its db. I see that there are several read group files that are produced by cuffdiff but cannot be downloaded in Galaxy. Is this the problem, and if so, how can Galaxy be used to generate data with (essential) replication? Are the p and q significance values reported in the output files a result of replicate analysis? I have tried to ask this question in several different forums without success. The responses I've gotten suggest its a Galaxy issue rather than either cuffdiff or cummerbund. I'm hoping someone here can help answer my questions. Hopeful, Mike___ 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/
Re: [galaxy-user] Problem with ftp connexion to Galaxy
Hello, If you account was created during a specific time window, then resetting your password is necessary. Instructions are in our wiki here: http://wiki.galaxyproject.org/Main/Notices#May_29th_2013_FTP_login_resolution Also, double check that you are using FTP, and not SFTP, from the command line. If problems continue, it would be very good to try a client such as Filezilla or Cyberduck (both are supported on Windows) to see if one of those permits a connection, to isolate the issue to the method rather than a user/password problem. Hopefully one of these helps to resolve the issue, but let us know. Please be sure to keep replies with the mailing list cc'd if more troubleshooting is required. Best, Jen Galaxy team On 7/29/13 7:57 AM, Fabrice BESNARD wrote: Hello, I registered some time ago to Galaxy. From the very beginning, my ftp connexion is not working. I am using Filezilla, on a windows operating system. More precisely, the connexion can be established, but the process fail when it is asking for the password. Statut :Résolution de l'adresse de main.g2.bx.psu.edu Statut :Connexion à 128.118.250.4:21... Statut :Connexion établie, attente du message d'accueil... Réponse : 220 ProFTPD 1.3.4b Server (Galaxy Main Server FTP) [:::128.118.250.4] Commande : USER fbesn...@biologie.ens.fr Réponse : 331 Password required for fbesn...@biologie.ens.fr Commande : PASS *** Réponse : 530 Login incorrect. Erreur :Erreur critique Erreur :Impossible d'établir une connexion au serveur I sent an email two month ago to report this problem. I was answered that this was an issue happening with the new accounts created. Obviously, this issue has not been fixed yet, has it? If yes, could you indicate me to make my ftp connexion works now ? Thank you for your help !! -- Jennifer Hillman-Jackson Galaxy Support and Training 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] rattus norvegicus reference genome
Hi I'm currently using the Galaxy pipeline to analyze my illumina chip-seq data. When I try to use NGA: MappingMap with Bowtie for Illumina to map my reads there is no rat reference genome. I says I should contact galaxy. Should I simply upload the genome to proceed with analysis? Thanks Matt ___ 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/
