I wanna see big picture and management of RNA-seq data like
1. quality of read: base calling, length of read,.......
2 screening: contamination, mismatch criteria,.........
3......
I have read research paper but do not understand well like it's very depend on researcher's criteria
I will appreciate it if reason of which step is discussed
and ready-to-use software for analysis is good enough. Do I need to learn about Linux things
RNA-seq beginner
thank you in advance
Hello,
After you do all of your qc investigations (FastQC, trimmomatic), then you must align the reads to the genome. RNAstar (https://code.google.com/p/rna-star/) is a good aligner, but some people like Bowtie or BWA. Then you can get differential splicing and differential gene expression with Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/releases/v2.2.1/) There are manuals for all of software. The genomes can be downloaded from UCSC (http://genome.ucsc.edu/). I know that this is a pretty brief post ,but most of this stuff requires a full reading of the manual in order to accomplish your goals. These tutorials helped me (http://homer.salk.edu/homer/ngs/index.html) Good luck!!
Hi
You need some basic linux knowledge which will really help you. There are many programs for trimming and filtering low-quality bases in your RNA-seq reads. I recommend you NGS QC toolkit or FastQC programs.
Hello,
After you do all of your qc investigations (FastQC, trimmomatic), then you must align the reads to the genome. RNAstar (https://code.google.com/p/rna-star/) is a good aligner, but some people like Bowtie or BWA. Then you can get differential splicing and differential gene expression with Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/releases/v2.2.1/) There are manuals for all of software. The genomes can be downloaded from UCSC (http://genome.ucsc.edu/). I know that this is a pretty brief post ,but most of this stuff requires a full reading of the manual in order to accomplish your goals. These tutorials helped me (http://homer.salk.edu/homer/ngs/index.html) Good luck!!
- Badges
- Science topic