Integrating open source SRA data sets with my own RNA-seq - what is the proper etiquette/tools for analysis?

Question

[ach140]

I am working on an RNA-seq experiment with my knockout mouse line to do a differential gene expression analysis of RNA extracted from brain tissue. Because this is not a conventional knockout study, I want to compare the gene expression profile of my study with that of other conventional knockout studies in mouse and from human cell lines to draw conclusions on the overall effect of this knockout. I've found a couple raw data sets on SRA, but I'm not clear on the exact etiquette of how to properly process, analyze, and present this data with my own in a way that's rigorous and intuitive for other researchers. Apart from obviously citing the raw data set and study that its from, I'm hoping to learn more on this process. If anyone has any suggestions of how to go about this and also what tools might be of particular help, I would greatly appreciate any comments.

Thanks

Answer 1

[colindaven]

I think you should look at a pipeline such as this from the excellent nf-core people. It might take a little to get up and running but is completely worth it.

https://github.com/nf-core/rnaseq

Then you can start experimenting with your knock out (if needed) by changing GTF files etc.

[ach140]

I will definitely look into this. Thank you very much!