3.3 years ago by
Double check your reference annotation file (GTF or GFF3). Make sure it has the attributes tss_id, p_id, and gene_name, for full statistics and incorporation of the annotation.
Also make certain that you use this at the Cuffmerge step, when combining the Cufflinks GTF datasets. Any transcripts not in the Cuffmerge results will be ignored when later running Cuffdiff.
The website for the Tuxedo pipeline has details about reference data and attributes. This is a good place to start:
I wasn't sure if this was a continuation of a previous conversation/Q&A, so apologies if this is duplicated info.
Best, Jen, Galaxy team