Thanks
Thanks for the info drio and krobinson.
Perhaps I'll see if the DNALinux people are interested in adding some of the NGS tools to the VM image and if so, I could build some of them in.
Ha, thanks for the "real programmer" comment. I tend to think of people who can write a video card driver in assembly as "real" programmers, but I guess that is the minority of even CS grads.
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I am interested in this as well but I do not find most reviews and papers I have read helpful as for learning. Does anyone know any tutorial that really explains the procedures in detail?Leave a comment:
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Bfast comes with a tool to generate synthetic reads (bfast/butil/bgeneratereads).Originally posted by Dave S. View Post
The software can introduce indels, SNPs, errors, etc...
bwa and maq have something similar too.
Figure out what is the current throughput from the different sequencers and generate data to "play" with it.
If you need to get closer to the sequencer, that is going to be more complicate. Start by downloading the manuals from your sequencer of choice and get the big picture of how the data flow happens.Leave a comment:
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Anyone who says they are fluent in 5 computer languages should quite saying they are not a "real" programmer!
The NCBI Short Reads Archive & European Short Reads Archive are good sources for datasets. Many of the programs will run on a typical laptop or desktop, though for really big datasets you will run into challenges.
Bowtie is a good first program to try.
There are several reviews floating around on second generation sequencing data analysis; one of the Nature magazines (Biotech? Methods?) had a special section recently. Or, just take one of the recent publications from the Literature Watch section here & read it end-to-end including the methods & try to digest that.Leave a comment:
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Dave - interested in trial data sets and high-throughput sequencing tutorials
Hi all:
I'm interested in learning how to analyze NGS data sets from the latest devices but have no access to the actual machines at my workplace. What are the best open sources of raw data to analyze?
I'd like to get up to speed on the essential NGS software and practice a bit with it. I am fluent in a couple programming languages (R, Perl, Java, C#, Python) but am not a "real" CS programmer (biologist by training).
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Developments in sequencing technologies and methodologies have transformed the field of epigenetics, giving researchers a better way to understand the complex world of gene regulation and heritable modifications. This article explores some of the diverse sequencing methods employed in the study of epigenetics, ranging from classic techniques to cutting-edge innovations while providing a brief overview of their processes, applications, and advances.
Methylation Detect...05-31-2023, 10:46 AM -
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
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