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2.4 years ago
Dhananjai
•
0
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
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.