Hi. I don't know if I may ask this here. I'm going to start my 3rd year in PhD study in a country where PhD study usually lasts for 3 years, and I feel that I haven't developed more skills than I expected.
I'm working on comparative genomics of a certain species of bacteria and my tasks include finishing the genome sequencing project (i.e., closing gaps by PCR & Sanger sequencing, which I have to say I don't enjoy, or by dry lab way using CLCgenomics to locally reassemble the reads with a reference genome), doing annotation (the actual functional annotation is done by my co-supervisor with his special pipeline, I do only ORFing and curating the pipeline output), and comparing the genome content to 1 to 3 closely related bacterium (I use OrthoMCL to find orthologous proteins and determine which bacterium doesn't have which protein). The results have been published in several genome announcements of a journal, and I still have to prepare "bigger" papers to explore more on the genomic comparison. However, I'm feeling that I haven't learnt enough.
When I see the requirements they're asking for postdoc positions, I'm terrified. Everyone asks for fluency in some programming languages, which I thought I will acquire while doing PhD (I learnt Perl & Java in my master's, but it was such a long time ago...), but I never need to do any programming up till now (or I've been too stupid to not know the contrary).
Am I being undereducated or is it just my feeling?
UPDATE: I'm happy to tell you that I have found an opportunity to use programming in my research, as I put in How To Know Percentage Of Identity Between Every Pair Of Orthologous Genes In Several Genomes?. I am planning to use Python to solve the problem.