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:Servicedesk@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 : fraud@kpmg.co.za For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za.
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.cufflinks@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:Servicedesk@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 : fraud@kpmg.co.za For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za.
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Lizex Husselmann