RNASeq analysis without reference genome using Trinity
Hi, I am new to the world of rnaseq analysis. I am using trinity for the analysis. I don't have a reference genome for mapping. I have the trinity output file. Which software I should use for rnaseq analysis without reference genome? Any help is appreciated. Thanks
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Dhananjai •
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It's hard to offer specific guidance without more information. What is the end goal of your analysis? You have a de novo transcriptome assembly from Trinity, but what are you looking to do with it?
I have the complete denovo assembly in the trinity.fasta output file. What I need is to do is mapping the RNAseq reads back to the assembly and then to calculate the transcript abundance.
Assuming you have got a set of fasta formatted transcriptome data from your trinity assembly, you can now use that newly assembled transcriptome with programs like
salmonorkallistoto start analyzing your data.