After reading this post http://software-carpentry.org/blog/2013/07/computational-competence-for-biologists.html, I realized that I am far from being competent....
currently, I know some python, R(bioconductor), linux commands, sed, awk, galaxy and feel comfortable to use command line based software like bedtools, samtools, bowtie etc. I still need to enhance my database skills though. More importantly, I will need to have some statistics knowledge.
I signed up for
Mathematical Biostatistics Boot Camp 1
a demonstration of the need to have good statistics knowledge:
Simon Anders from EMBL has very good slides about statistics behind RNA-seq analysis.
see post here http://www.rna-seqblog.com/presentations/comparative-analysis-of-rna-seq-data-with-deseq-and-dexseq/
I quite agree that bioinformatics is pretty much about visualizing the data and finding patterns. So, I will need to master skills to clean data, transform data and visualize them. R has very good packages to generate figures and matplotlib from python is also worth learning. Sometimes, I am confused with R and python pandas package. manipulations of matrix and dataframe in these two different languages are somewhat similar but still different...I have to switch my thinking mode back and forth....
Anyway, I still have a long way to go, and I know I can not learn everything, but I can learn anything that I need at that moment.