Hello!

                I have an RNA-Seq project which consists of 5 samples from the species tree shrew.  When uploading these fastq files into Galaxy, I chose “unspecified (?)” for the database/build since the latest tree shrew version is not in the drop down list.  When using TopHat, Cufflinks/Compare I have selected a reference genome from my history instead of using a built-in index, as well as a gtf annotation file for Cufflinks/Compare and everything has been working fine.  Now, I am at the Cuffdiff step and I am running into an error when setting it up to perform replicate analysis.  When I select my TopHat accepted hits bam file I see a red X and the error: “Unspecified genome build, click the pencil icon in the history item to set the genome build.”  Here’s a screenshot of what I’m seeing:

                Since the latest reference genome for tree shrew wasn’t listed, that’s why I chose “unspecified (?).”  Should I go back and edit these accepted hits bam files to say the Database/Build from the drop down list is “Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1)?”  I know that this is simple to change, but will this affect my results in any way?  Any help/info would be greatly appreciated.

Thanks,

David