[galaxy-user] CUFFLINK does not work!
Hello Di Nguyen, Without seeing your history, my initial guess is that the SAM output from the mapping runs need to be sorted before running Cufflinks. (Tophat, which is designed to map spliced RNA-seq data, sorts the SAM output as part of the data processing, but BWA and Bowtie do not). The workflow provided on this FAQ can be followed to sort SAM files for Cufflinks: https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq2 If you continue to have problems, please submit a bug report (click on green bug icon from the error Cufflinks dataset as run on the main public Galaxy instance (http://usegalaxy.org), leave all inputs and the error dataset undeleted, note this email address in the comments if it differs from your Galaxy account email address (so that I can link the two issues together), and we can provide more feedback. http://wiki.g2.bx.psu.edu/Support#Error_from_tools Hopefully this helps, Jen Galaxy team On 6/20/12 1:28 PM, Di Nguyen wrote: Hi Jen, I mapped with BWA and Bowtie for my RNAseq but Cufflink DID not run. This is the error message: An error occurred running this job: /cufflinks v1.3.0 cufflinks -q --no-update-check -I 30 -F 0.10 -j 0.15 -p 8 -b /galaxy/data/hg19/sam_index/hg19.fa Error running cufflinks. return code = 1 cufflinks: /lib64/libz.so.1: no version information available (required by cufflinks) /What should I do?/ Di Nguyen / -- 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] Cufflink
Hello Ateequr, To confirm, you are working on the main public Galaxy instance at: http://usegalaxy.org (https://main.g2.bx.psu.edu/)? There are at present no known problems with Cufflinks. If your datasets are not recognized by the tool, then a double check that the datatype is assigned correctly is the first place to start. Click on the pencil icon for the datasets and on the 'Edit Attributes' form, scroll down to datatype, and assign if necessary. BAM data is somewhat difficult to load or have in a history without having it detected and assigned - so that is likely a problem. But a reassignment to tabular can occur for SAM data, if you have been performing text manipulations on the data and do not have headers. Just confirm format and change the dataset assignment back to SAM so that Cufflinks will accept it as input. A metadata error (presented in a yellow box within the dataset) may be an indicator that something is wrong, although one round of 'attempt to manually correct' using the link provided is good to try and can often correct the issue. Hopefully this helps, Jen Galaxy team On 4/30/12 7:12 AM, Ateequr Rehman wrote: Just wanted to make sure if cofflink is working or not cufflink is not detecting my SAM or BAM files., ___ 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://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] Cufflink error
Hello Lizex, The primary reason why runs fail is the input data format. A double check that the reference genome identifiers are the same between the BAM files and any reference GTF files would be recommended. This and other common issues are covered in our FAQ here: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq If you think that the Tophat run was a problem, then contacting the tool authors at tophat.cuffli...@gmail.com is the best way to get help with a Tophat issue, especially if run line-command outside of Galaxy. http://tophat.cbcb.umd.edu/ http://cufflinks.cbcb.umd.edu/ If you are still stuck, please send a bug report using the green bug icon for the error dataset and we can take a look. Please put in a note if the email address for your Galaxy account is different than this one. Thanks! Jen Galaxy team On 11/7/11 11:33 PM, Lizex Husselmann wrote: Hi I've started an alignment using the command line (Tophat v1.3.3). I've uploaded the files (accepted.bam) onto Galaxy and upon doing the Cufflinks analysis on the Galaxy interface, it shows an error. I had to look at the options. I've change the options to default and run it again but still the same error. Is the accepted.bam file not compatible with the Galaxy Cufflinks? Is there something I not doing? Kind regards Lizex Disclaimer This message is confidential and may be covered by legal professional privilege. It must not be read, copied, disclosed or used in any other manner by any person other than the addressee(s). Unauthorised use, disclosure or copying is strictly prohibited and may be unlawful. The views expressed in this email are those of the sender, unless otherwise stated. If you have received this email in error, please contact ARC Service Desk immediately. (mailto:serviced...@arc.agric.za) To report incidents of fraud and / or corruption in the ARC use our Ethics Hotline by: Phone number : 0800 21 20 56 Fax number : 0800 200 796 Email address : fr...@kpmg.co.za For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za. ___ 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/
[galaxy-user] Cufflink error
Hi I've started an alignment using the command line (Tophat v1.3.3). I've uploaded the files (accepted.bam) onto Galaxy and upon doing the Cufflinks analysis on the Galaxy interface, it shows an error. I had to look at the options. I've change the options to default and run it again but still the same error. Is the accepted.bam file not compatible with the Galaxy Cufflinks? Is there something I not doing? Kind regards Lizex Disclaimer This message is confidential and may be covered by legal professional privilege. It must not be read, copied, disclosed or used in any other manner by any person other than the addressee(s). Unauthorised use, disclosure or copying is strictly prohibited and may be unlawful. The views expressed in this email are those of the sender, unless otherwise stated. If you have received this email in error, please contact ARC Service Desk immediately. (mailto:serviced...@arc.agric.za) To report incidents of fraud and / or corruption in the ARC use our Ethics Hotline by: Phone number : 0800 21 20 56 Fax number : 0800 200 796 Email address : fr...@kpmg.co.za For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za. ___ 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/
