Question: Trinity : How To Co-Assemble Different Samples (Tumor And Healthy)
3
gravatar for Nicolas Rosewick
7.5 years ago by
Belgium, Brussels
Nicolas Rosewick8.0k wrote:

Hi,

I'm using Trinity to assemble RNAseq data (2X76bp) from an non-model species without available genome. I'm studying tumor samples. For this, I've three control samples (healthy cells) and 9 tumor samples. To perform differential expression analysis (with DESeq or edgeR per example) after the assembly, I've to co-assemble all the samples at once (so concatenate all the fastq files in one big fastq file and perform trinity on it)

Is that right ? Even if the tumor cell can have a totally different transcriptome (genetic modification, etc...)

Thanks a lot for your advices.

trinity assembly transcriptome • 3.2k views
ADD COMMENTlink written 7.5 years ago by Nicolas Rosewick8.0k
3
gravatar for Rt
7.5 years ago by
Rt80
Rt80 wrote:

Your understanding is correct! It should be more clear on Trinity documentation.

Here is Brian J. Haas's explanation:

"The general idea is to combine all your rna-seq data and generate one assembly. Then, to align the reads from the different samples separately to the Trinity assemblies, computing abundance estimates based on each read set. Finally, you do the differential expression analysis to identify those Trinity assemblies that are of interest. This is all outlined in the downstream analysis section of the documentation. If there's still some confusion about this, let's continue to work through it."

ADD COMMENTlink written 7.5 years ago by Rt80
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