hi everyone, I am new to NGS analysis field. I have RNA seq data of a plant after infection and healthy plant data at three stages. What insilico analysis can be done with this data and what softwares can be used. Can anyone guide me with this.
If you are new to NGS data analysis take a look "https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification" . Its quite easy and well documented. If you are not comftable with programming, then you can try Chipster, a online tool for NGS data analysis
Here are 2 papers from Nature Protocol may help you
tophat + cufflinks: http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
hisat + stringtie: http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html