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Does anyone know what the exact primer sequences are for the cancer panels? I really need to know so I can remove them during the alignment step. Otherwise it causes certain indels to be missed.
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Hi there,
After logging in to the AmpliSeq Designer website, navigate to the Ion Panels page. From there you can choose to 'Download panel files" for the panel you need. The pop-up window describes the contents of all the files in the zip archive, including the *.primerDataSheet.csv file to which you are referring.
I would also recommend follow up with your local Field Bioinformatics Scientist if you have any questions about analysis of the data with which they may be able to assist.
Originally posted by RockChalkJayhawk View Post -
Thanks Torrent!Comment
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aren't the majority of the primer sequences removed in the library protocol?Comment
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Not sure. All I know is that there are several 9-15bp indels that are Sanger validated that are not getting aligned. I know BWA will not usually align reads with indels > 8bp, but Novoalign does. Basically, I'm trying to develop a "Best Practices" workflow for high coverage amplicon sequencing. Too many assumptions are invalid if we use the workflow for 30X exome.Originally posted by snetmcom View PostComment
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are you using the ampliseq analysis template? i would assume it handles this data with tmap.Comment
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Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
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With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
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