resently we submited some samples from zebrafish to do a rnaseq (Novogene), the problem was that due to our low understanding of the process, we got a denovo analysis (for species without a reference). My question is if it is posible to get diferential expression data from that type of analysis?
thanks in advance
Follow those articles :
https://www.creative-biolabs.com/suprecision/whole-transcriptome-sequencing-service-for-cancer.htm?gclid=Cj0KCQjwhtT1BRCiARIsAGlY51JLMbzURyh2XKn8ufq3UqD0JnZAQN6c2Wx8G9sAj9l843SpGdQzOakaAopwEALw_wcB
https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/de-novo/tutorial.html
https://www.nature.com/articles/s41598-019-42560-9
https://www.hindawi.com/journals/ijg/2013/269191/
https://www.1010genome.com/de-novo-transcriptome-assembly-and-differential-gene-expression-analysis/
what is they type of data you have received post de novo RNAseq ? It depends on the format of the data you have received and how to go forward with that. I wonder why the sequencing company did not provide sufficient information before you started the entire process.
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