Entering edit mode
2.7 years ago
Ashish
•
0
I have been provided a task of developing a RNA Seq pipeline, but since there are so many tools and pipelines already available, I am not able to figure out how my pipeline would be superior that the existing ones.
Please suggest some useful literature that can help me with this task.
Unless you are doing something very non-standard that requires special code then the answer is most likely that you're reinventing the wheel. Just use something like https://github.com/nf-core/rnaseq and be done with it, spend the saved time on the actual science.
A good argument to write your own stuff would be though that you are free to add new feature at will. For nf-core for example (or any other workflow community) if you want new features added then you ask the nf-core people for it. Usually that works fine, but if for any reason they reject your request (just hypothetically, for the sake of this argument here) then you are stuck because adding something yourself to such a complex infrastructure is hard (maybe even impossible) unless you spend days or weeks working yourself into the internals of the pipeline. Same goes for snakemake (e.g. SnakePipes) or any other workflow collection. So I would critically think about whether you really need to develop something from scratch.
Got a feeling OP just needs to do DE analysis but unfortunately got saddled with the term "RNA-seq pipeline" by their supervisors/collaborators.
Hi ATpoint,
Thank you for your answer! I am in the same situation as the author of this post and I wonder why people want to build a new RNA-Seq pipeline to customize it? Is that for learning purposes? What is the possible advantages of this task?