Question: Merging de-novo transcriptome assembly from multiple datasets
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gravatar for gil.hornung
16 months ago by
gil.hornung60
European Union
gil.hornung60 wrote:

Hi,

I have a new dataset of Illumina RNA-sequencing from an organism without a known genome. I have two more older datasets from the same organism (different protocol and different machine). I want to build a de-novo transcriptome assembly based on all the data (I plan to use Trinity). The question is whether to pool all the data together or run the assembly independently for each dataset and then combine the results in some way.

Does anyone have experience with this?

Thanks,

Gil

transcriptome assembly • 551 views
ADD COMMENTlink written 16 months ago by gil.hornung60

What type of data do you have? Do you plan to do DGE? Trinity recommends building a single assembly with combined data. You can specify replicates/samples downstream for DGE analysis.

ADD REPLYlink written 16 months ago by st.ph.n2.3k

I have paired end illuminia sequencing. The two datasets are from the same organism, although not necessarily from the same isolate. There are differences in the length of the reads 125 or 100) and the Illumina machine model

ADD REPLYlink written 16 months ago by gil.hornung60
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