There are 2 loci in a genome that are separately annotated and were thought to be two separate genes. Experimental evidence from cDNA sequencing now confirms that they are actually one gene. Now I need to modify the .gff and .fa files and re-do bowtie/tophat/cufflinks analysis to find corrected expression values for this combined genes. I have a few questions for this.
Column 8 refers to: "frame - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on.." What's the best way to determine what this should be? I could do it by eye, but is there software that is best for this?
Is there software that I can use to use my CDS sequencing data to generate corrected data for these .gff and .fa files? Is the best way to modify these using a text editor?
Thanks for the help.