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It has been a long time and I don't remember exactly, but I think I solved the problem by trimming the polyG at the end of reads. -
Hi did you got any solution? I am stuck in the same position and trying to figure outLeave a comment:
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Problem with DRAGEN Bio-IT Platform
I have a problem with DRAGEN Bio-IT Platform.
When I ran the map/alin and valiant caller pipeline, it stopped running by time out error.
I asked to illumina technical support, and changed the usage memory amount using this option.
" --bin_memory 60000000000 "
However, this option and more usage memory (200,000,000,000) did not solve the problem, and error was printed as below.
" The DRAGEN WatchDog service has detected a fault: Available free memory (1518 MB) is below minimum threshold (2048 MB) required by DRAGEN "
I have enough memory server and I did not run any other scripts at the same when I ran DRAGEN pipeline.
This probrem was happened when I input 193 Gbyte fastq.gz file.
Could you tell me how I can solve this problem and/or the cause of this problem?
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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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