TL;DR Run a RNA-seq pipeline using Snakemake locally and later port it to Google Cloud. Snakemake can parallelize jobs of a pipeline and even across machines.
Snakemake has been my favorite workflow management system for a while. I came across it while writing my master thesis and from the …
本文內容主要來自 Barak Cohen 教授給的數堂課的筆記，以 Systems Biology 的角度來看 coding/noncoding variant modeling 和相關實驗 MPRA。
Using fundamental R/Biocondcutor packages (e.g. AnnotationHub, ensembldb and biomaRt) to query Ensembl genomic references or annotations.
TL;DR Plot exome sequencing depth and coverage with genome annotation using Gviz in R. Then apply detail control on Gviz annotation track displaying.
This is an extending post from Genomic Data Processing in Bioconductor, though I haven’t finished reading all the reference in that post. The background knowledge …
Notes of fundamental tools and learning resources for handling genomic data in R with Bioconductor.
This post demonstrates the FASTQ to FASTA conversion and sequence quality check using seqtk.