RNAseq

quality control of your fastq file! my first post after I got my PhD!

I passed my defense on Tuesday, and now I am a PhD! what a long process, it took me six years. I’ve been enjoying the PhD experience though.

DESeq work flow

I was working on a human RNA-seq data set, and I already got the count matrix by HTSeq.\ see my previous post here RNA-seq analysis samtools sort and…

RNA-seq analysis samtools sort and htseq-count

I am following the RNA-seq nature protocol from Simon Anders. See my previous post here:Two nature protocols for RNA-seq analysis

Tophat run time

It took me 45 hrs to map a 24G single-end RNA-seq data to human hg19 with the gtf file from GENECODE!

Detect mutations from RNA-seq data

Usually we detect mutations by DNA-sequencing or whole exome sequencing, GATK is the commonly used pipeline for this purpose.

FPKMs and counts compared for RNA-seq data

A very nice article comparing FPKMs and raw counts in RNA-seq data analysis

RNA-seq step by step demonstration

Align RNA-seq with Tophat

Two nature protocols for RNA-seq analysis

One is from Simon Anders, his group wrote the DESeq

DESeq2 is now in Bioconductor

Thank you Simon and your team!

sashimi_plot for RNA-seq data

It is a python package for visualizing the RNA-seq data.