Resource for hands on experience

Question

[irfanwustl]

Hi, I am from computer science background. As I am new to bioinformatics I am wondering is there any resource (book, workshop, blog, online course, etc) focusing on practical aspects of the different biological data? Particularly is there any resource on how to process expression data (both array based and NGS based RNA-seq) and methylation data (450k array, WGBS, and RRBS)? It seems I am comfortable with the machine learning part but I have issues with the preprocessing part like do I have to normalize WGBS based bedgraph file or not? I feel that I need a hands-on tutorial on these parts. It will be very helpful if you give me some suggestions? Mainly what to do after getting the fastq files.

Answer 1

[ATpoint]

For RNA-seq I recommend:

https://peerj.com/preprints/27283/

https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

plus the user guides / manuals of the Bioconductor tools DESeq2, edgeR and limma. All commonly used for RNA-seq (limma for arrays) with plenty of background information and example code.

For methylation analysis (differential methylation) there is also a section in the edgeR manual afaik. Other tools worth reading about towards alignment and methylation calling could be Bismark, bwa-meth and MethylDackel. Those were the ones immediately coming to my mind, haven't worked on methylation in quite a while so others probably have better suggestions.

Please be sure to use the search function as well, there are many threads on these topics already.