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Originally posted by maubp
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Really thanks, maubp. The problem solved~! -
The same for 500bp reads where the default is better for 0-2% error rates.Originally posted by aleferna View PostComment
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I have got somewhat related question, how do I tweak gsMapper parameters in order to get the reads mapped without introducing gaps. I am looking for SNPs and InDels and the gsMapper output (454AllDiffs.txt) shows gaps rather than mismatches. The mappings to the reference sequence looks fine, but when it comes to detecting variants the mapper is not doing what I expected it to do. Is there some extra step that I am missing for SNP/Indel detection? I have also tried AVA, but as my sequence is not an amplicon (far too big than the standard definition of amplicon in 454 terms), AVA isnt of much help either.Comment
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Hello Everybody
I would like to know if it is better to use 1 or more reference genome at a time, using the reference gs mapper, for 454 reads
Thank YouComment
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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.
...06-02-2026, 10:05 AM -
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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