Project suggestions with paired Tumour and Normal RNA Seq data libraries

Question

[mandhirsikander]

I am a Bachelor's student and as part of my 3 month project I have to work around Paired Gastric Cancer Tumour and Normal RNA-Seq data libraries. I am looking for anys suggestions on what can I do as part of my project.

[ATpoint]

I think this is completely the wrong approach (please take this as constructive criticism and not as offence). As an unexperienced Bachelor student you will have to spend quite some on the technical details like using alignment and downstream analysis software. You should ask your supervisor for a well-defined and managable project that allows to be completed in time while niehter over- nor underdemanding you. Planning this is beyond your scope right now (at least it was for the guys I've met during my short career so far simply because you lack the experience and tend to underestimate the necessary effort.) I strongly recommend to sit with your supervisor and open-mindedly discuss the options.

[mandhirsikander]

Thanks for the reply! I have been trying to work at MSI detection but I have hit rock bottom and not able to proceed hence it is a desperate approach I have been forced to try.

[Bastien Hervé]

Is it not part of the project to search for RNA-seq applications ? I let you this link (which is just googled "applications RNA-seq"), pick one application and look for associated papers, then cross materials & methods to make your own pipeline fitting your data.