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We are a core facility that receives samples from multiple labs. We have one lab in particular that submits which are ran on a 3730XL. We are trying to determine what is happening with these particular results. The first time that we run their plate the results don't look particularly good but if we put that same plate back into the ABI we see a much better signal. I've spoken with another facility who thought it was due to some contamination. I don't really know where this would be coming from as we run the bigdye reaction and cleanseq on all the plates and it's only seen with this particular lab's plates. I would really like to try to help troubleshoot this issue for them. I have attached images of the first and second run. Subsequent plates look pretty good on the first run but could also be improved on the second run. These are also being ran back to back.
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If the second run from the same plate is better, also the signal is declining with reads length, than it is salts being injected instead of labelled DNA fragments on the first run.
I would suggest to use 200ul of 70% ethanol during the ethanol wash stage (if using ethanol precipitation in plates for sequencing reaction products purification). If doing precipitation in 1.5 ml tubes - than use 1ml of 70% ethanol on the wash step.
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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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