I am working with cufflinks programs but I have different problems.
1.- Fist I used only cuffdiff without cufflinks, since I have D.melanogaster transcripts and in theory I can do that because is a well annotated organism. But in the results I have the cds.exp.diff file empty Why?
2.- After that I use Cufflinks (using the genome.fa and genome.gff options) and I have the transcripts.gtf outputs but also have message like that "Error (GFaSeqGet): end coordinate (1050) cannot be larger than sequence length 1049". It is importan? or I can omit that?
3.- I run cuffmerge with the "transcript.gff" and I have the merged.gff file, but also have again messages like Error (GFaSeqGet): end coordinate (2921) cannot be larger than sequence length 2916.
4._ I run cuffdiff using the merged file, the program run and I have my files but some of them are empty as CDS files
What is happening. I'm going crazy