Question: Should I merge all fastq files from different conditions for transcriptome assembly or not?
gravatar for Gustavo
2.7 years ago by
Gustavo0 wrote:


I have RNA-seq data from 4 experimental conditions, each one with 3 replicates, and my primary goal is differential expression. My doubt is if combining all the samples into a single input target for the transcriptome assembly would be recommended for all assemblers.

I was using Trinity and they do suggest to combine all samples into a single fastq file for performing the analysis. However, I also want to test other methods (such as SOAPdenovo-trans, Oases). Unfortunately I couldn't find clear information if merging the fastq files would also be recommended for them. If not, why?


rna-seq assembly • 1.2k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 2.7 years ago by Gustavo0

This post might help: Trinity : How To Co-Assemble Different Samples (Tumor And Healthy)

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Sej Modha4.4k
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