Hello, I have a question regarding cufflinks. I used HISTAT2 for alignment using this file - c_elegans.PRJNA275000.WS263.genomic.fa Then I ran cufflinks with this annotation file c_elegans.PRJNA275000.WS263.annotations.gff3.gz
I get FPKM values but no gene names. What happened? I thought that since I got the alignment reference and the annotation from the same source they should work?