Galaxy is an extremely powerful web tool for many bio-informatics analysis, with the recent inclusion of Trinity and blast, It has never been easier to conduct a full RNA-seq pipeline Galaxy. In this video, I include a simple walk through on how to
1. Download fastq from NCBI SRA database
2. Combined multiuple fasta into a single file
3. Feed the raw fastq into Trinity for contig assembly
4. Annotate the de novo transcriptome using a cDNA database downloaded from ensemble
5. Count transcript expression level in the two individual sample
6. Export results into text file onto local computer
together some simple explanation on how and what does each of the tools does, and why do we use them in the analysis
References:
Salmon:
https://combine-lab.github.io/salmon/
Galaxy
https://usegalaxy.org
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