January 2023

Top Bioinformatics and Genomics Blogs

1. Diving into Genetics and Genomics: A wet-dry hybrid biologist's take on genetics and genomics. Mostly is about Linux, R, python, reproducible research, open science and NGS.

Diving into Genetics and Genomics

2. Genome Spot:  Practical tips for genome analysis and genomics data managment.

Genome Spot

3. DNA CONFESSES DATA SPEAK: How to handle large-scale genomic data and pipelining workflows.


4. Xiaole Shirley Liu's Blog Site: Computational Genomics, Translational Cancer Research, Big Data Mining.

 Xiaole Shirley Liu's Blog Site

5. Gigabase or gigabyte: An overview of bioinformatics and Genomics projects with links to relevant pages and posts.

Gigabase or gigabyte

6. The Genome Factory: Bioinformatics tips, tricks, tools and commentary with a microbial genomics bent. Written by Torsten Seemann from Melbourne, Australia.

The Genome Factory

7. RajLab: Random musings from the Raj Lab for systems biology.


8. Omics! Omics! A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery.

 Omics! Omics!

9. Next-Gen Sequencing: A working guide to the rapidly developing world of Next-Generation DNA sequencing, with an emphasis on bioinformatics.

Next-Gen Sequencing

10 Blasted Bioinformatics!? Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too.

Blasted Bioinformatics!?

11. Mike Love’s blog: How to analyse NGS data and about differential expression analysis tools DESeq2 and edgeR.

Mike Love’s blog

12. Bioinformatics Zen : A blog about bioinformatics and mindfulness by Michael Barton.

Bioinformatics Zen

13. KidsGenomics : This blog will instead focus on genetic diseases that affect children, including rare inherited disorders and pediatric cancers.


14. Kevin's GATTACA World: My Weblog on Bioinformatics, Genome Science and Next Generation Sequencing.

Kevin's GATTACA World

15. Charles Warden's Science Blog A blog about genetics, genomics, and personal opinions about science research.

Genomics, ETC.


Practical tips:

Basic STAR alignment commands:

Building the STAR index (–runMode genomeGenerate):

STAR --runMode genomeGenerate --genomeDir igenome/hg19   --genomeFastaFiles Sequence/hg19.fa --sjdbGTFfile annotations/hg19.gtf  --sjdbOverhang 50 --outFileNamePrefix hg19

Aligning reads to the genome

STAR --genomeDir igenome/hg19 --readFilesIn rawdata/Sample_1.fastq.gz rawdata/Sample_2.fastq.gz  --readFilesCommand zcat  --outSAMtype BAM SortedByCoordinate  --quantMode GeneCounts  --outFileNamePrefix Sample_GroupX

Read counts:

Run using bash scripts:


# define variables


# get our data files


for f in $FILES


echo $f

base=$(basename $f .fastq.gz)

echo $base

STAR --runThreadN 3 --genomeDir $index --readFilesIn $f --outSAMtype BAM SortedByCoordinate  --quantMode GeneCounts --readFilesCommand zcat --outFileNamePrefix $base"_"


echo "done!"


An extensive resource for Bioinformatics, Epigenomics, Genomics and Metagenomics