RNASeq analysis without reference genome using Trinity

Question

[Dhananjai]

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

[Dave Carlson]

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?

[Dhananjai]

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.

[GenoMax]

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 salmon or kallisto to start analyzing your data.