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About the second question, what do you think is the best approximation to perform the analysis? smallRNA-seq or total RNA-seq? -
Not directly able to answer you question (in this case how do you define significant "depth"? A single read, could (in theory), represent a real rare RNA).
There are many "exosome" labeled datasets in SRA: http://www.ncbi.nlm.nih.gov/sra/?term=exosome You may want to look through those and associated publications (if any).Leave a comment:
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Other question. My bosses said to me that in literature has been reported that the exosomes can contain some mRNA molecules. To exosome profiling is more suitable using total RNA-seq (smallRNA + mRNA) or only smallRNA-seq?
thanks in advance!Leave a comment:
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Coverage dept needed for Exosomes
Hi all,
In my lab, we want to characterize (only characterize, not differential expression) RNA elements inside of exosomes, by using sequencing. My bosses want to make a pool of several samples.
I think is different than conventional RNA-seq because we aren't going to use all the transcriptome, only the exosomes.
Do you have any idea of the minimum depth needed for this kind of analysis?
Thanks in advance!Last edited by diego diaz; 05-04-2015, 07:26 AM.
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Differential Expression and Data Visualization: Recommended Tools for Next-Level Sequencing Analysis
After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...05-23-2023, 12:26 PM -
Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.
Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50...05-19-2023, 10:03 AM -
With new tools and computational resources being released regularly, it can be hard to determine which are best suited for the analysis process and which older tools continue to be maintained. In an effort to assist the sequencing community, we interviewed three highly skilled bioinformaticians about their recommended tools for several important analysis applications.
Quality control and preprocessing tools
“Garbage in, garbage out” is a popular...05-16-2023, 10:11 AM
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