My experience with Bioconductor I been involved with the Bioconductor project for several years and last year I attended the BioC2019 conference in New York. It was my first time in an international conference abroad. I'm posting here my experience with the project. Pre-conference The first time I heard about Bioconductor was in 2013 when in an internship, my main goal was to analyze data from Pichia pastoris and look at the functions of the differentially expressed genes through gene ontology. I did it with topGO and other packages included in Bioconductor. Later during the master in Bioinformatics for Health Science I studied, we used several packages from Bioconductor to analyze other data (the main project is still online ). Also as part of the master thesis I also used some other packages (the thesis involved using WGCNA ) but the main question roadblock was knowing the function and what are the genes doing. So I developed a package to compare the annotation of genes accord...
Here I'll share some experiences for sequencing samples by RNA. Most of them will be useful for other techniques and also for single cell sequencing (or scRNA-seq). Here I'm assuming that you do a short-sequence technique from Illumina or similar companies. Also I'll provide some tips to make easier the life of the bioinformatician that will analyse the data. Don't expect to find how many reads for sample you need or which design is better or which machine. Neither I will talk about prices or provide a list of companies and scientific platforms to look for. I won't cover how to analyse the data, or compare pipelines to process RNA-seq. Hope this post is more practical than all that but less technical. Before sending: Get ready You carried out your experiments and have already extracted the RNA from patients, mice, rats, cell cultures or whatever are you studying. You have them named with sensible names for your experiment like A+B-, 4789/Diff, 256-w046 and u...