Transcriptome assembly: single individual or pooled samples
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Marianna • 0
@7cc5052f
Last seen 7 days ago
Italy

Dear colleagues,

I'm going to set up a RNA-seq experiment to characterize the transcriptome of different tissues of a species with a published genome in ncbi (but not a model species...). The aim is to characterize the tissue-specific transcriptome, evaluating eventual alternative splicing events. I'm going to make a 150 PE seq with a good coverage (at least 50M reads). The idea is to start from 3 pooled samples for each tissue in order to represent also variability occurring in different animals (what if a gene is not expressed in an individual for its specific conditions/characteristics?).

Going to the question: based on your experience, do you think that state-of-the-art transcriptome assembly softwares might have "problems" with reads coming from different animals? I'm thinking about polymorphisms... This should not be a problem, having a reference genome, isn't it?

Thank you in advance for your time and suggestions

Best

Marianna

transcriptome splicing assembly • 48 views
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@james-w-macdonald-5106
Last seen 23 hours ago
United States

This support site is intended to help people who have technical issues with Bioconductor software. Your question has nothing to do with Bioconductor, so you should instead try posting at biostars.org, where your question will be on target.

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