Recently I've been tasked to count the numbers of gene isoforms for each locus in a
.gff3 file. I'm still doing my first steps in biology and bioinformatics, so I still struggle with some concepts and methodologies.
According to my understanding a gene isoform is a mRNA located in the same locus but with different start positions, so I did the following procedures:
- Selected the entries in the
.gff3that are classified as mRNA.
- In my
.gff3there is the additional information of the locus of the mRNA, so I checked for each locus how many unique values there were for the Start values and subtracted one.
- Assigned each value from step 2. to their respective locus, resulting in the desired number of isoforms for each locus.
My question is is this method correct?
Why do I believe it could be wrong or inaccurate: I don't have a complete solid understanding of a gene isoform, and researching some more I've seen that not only the start point of the mRNA is relevant but other things such as the protein coding DNA sequence (which I believe could be identified in the file under the CDS tag) and untranslated regions (which I don't know if I can identify in my file), and in the method I described above I've only taken in consideration the Start position, what appears to be incomplete.
Additionally if the method is incorrect how can I take in consideration the additional circumstances, and if it's correct why didn't those circumstances influence the count so much?