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.
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.
6. The Genome Factory: Bioinformatics tips, tricks, tools and commentary with a microbial genomics bent. Written by Torsten Seemann from Melbourne, Australia.
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.
9. Next-Gen Sequencing: A working guide to the rapidly developing world of Next-Generation DNA sequencing, with an emphasis on bioinformatics.
10 Blasted Bioinformatics!? Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too.
11. Mike Love’s blog: How to analyse NGS data and about differential expression analysis tools DESeq2 and edgeR.
12. Bioinformatics Zen : A blog about bioinformatics and mindfulness by Michael Barton.
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.
15. Charles Warden's Science Blog A blog about genetics, genomics, and personal opinions about science research.
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:
#!/bin/bash
# define variables
index=/home/BG/Align_STAR
# get our data files
FILES=/home/BG/rawdata/Sample_*.fastq.gz
for f in $FILES
do
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"_"
done
echo "done!"