Can I perform de novo analysis on RNA seq file of Mus musculus?

Question

[rprog008]

Dear member, I got some interesting SRA file of Mus musculus related with my work in SRA database. Original authors have utilised Trapnel protocol for their analysis and found some interesting result but I found some lacuna, like no analysis of long non codind RNA analysis. I want to re-analyse the same data with de novo analysis via Trinity and want to add some more analysis. My question is, is it worth doing ? because already the original authors have done the work. Again, Mus musculus is having its own reference genome, so why shall i go for de novo? What is the benefit of de novo analysis over other method.

WIll the data be publishable if i re-analyse it. I know it depend on reviewers as well as editor and thus seeking suggestion to you all.

Both positive and negative comments are welcome.

Thanks in advance :)

[rprog008]

Thanks @kristoffer and @JC for your reply.

@Kristoffer.. This workflow look great. I will try.

One question i have .. will it be ok, if i assemble transcript file using Trinity and annotate those transcript with mouse genome.

[Kristoffer Vitting-Seerup]

Trinity is better for unannotated genomes. For annotated genomes it is much better to use Cufflinks or StringTie via the workflow I sugges in this section of my vignette.

Answer 1

[JC]

Of course you can do the analysis again, either using updated programs and references or with the de novo assembly, many sequences could be discovered just because nobody wasn't looking for it.

Answer 2

[Kristoffer Vitting-Seerup]

I would argue that you should always use the "guided" approach when you already have a well annotated genome. With regards to updated pipeline I have a description of the workflow here where especially the new merging tools (or analysis of all samples simultanious) seems to give an advantages over the original Tuxedo pipeline.