I have been trying to figure this out for the better part of a week so hoping someone has had the same issue. I am using the cufflinks -> cuffmerge -> cuffdiff pipeline for RNAseq data. For cuffmerge I used both the mm10.gtf reference file as well as a genome .fa file. The output from cuffdiff is only giving gene names to comparisons that give a NoTest status. Anything that was tested wether significant or not has no gene name given to it, obviously I am most interested in significantly different gene expression so the information I want most is not being given. I do not know what would make the program give notest transcripts the matching gene name and actually tested transcripts no name. Please let me know if anyone has a solution to this or even just something I could try as right now I am completely out of ideas.
Thanks in advance!