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Fabulous! Please link to the datasets, and I'll try to put wheels in motion via the wiki :-) -
There is and we have these datasets already. I would be happy to share. We did a number of tests with this dataset for a manuscript we are sending out.Leave a comment:
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Simulated reads from real genomes.
We could simulate a range of 'noise' across a series of error models and produce reads characteristic of a variety of technologies... there must be software to do this already right?Leave a comment:
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Should we generate data so we have a 'gold standard'? Or just work with metrics based on consistency, speed, and coverage?Leave a comment:
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I'd recommend using % reads mapped and the # of reads mapped uniquely as part of the evaluation, and keep in mind that the # of known heterozygotes is a measure of sensitivity, NOT accuracy. My two cents.Leave a comment:
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Cool! It shouldn't be too hard either, but we need to have clear guidelines about what to measure and how, so that results are comparable across mappers. The only other thing we need is a dataset and a place to host it...Leave a comment:
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That would be AWESOME! I think we should query SEQanswers folks and vote on a number of metrics... this would be fun group project...Originally posted by dan View PostLeave a comment:
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I was thinking to organize a 'mapathon' on the wiki.... how would you recommend benchmarking accuracy?Leave a comment:
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HTS Mappers!
Anyone vounteer to update the wiki ;-)
Motivation: A ubiquitous and fundamental step in high-throughput sequencing analysis is the alignment (mapping) of the generated reads to a reference sequence. To accomplish this task numerous software tools have been proposed. Determining the mappers that are most suitable for a specific application is not trivial.
Results: This survey focuses on classifying mappers through a wide number of characteristics. The goal is to allow practitioners to compare the mappers more easily and find those that are most suitable for their specific problem.
Availability: A regularly updated compendium of mappers can be found at http://wwwdev.ebi.ac.uk/fg/hts_mappe...g/hts_mappers/.
Contact: [email protected]
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Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...09-07-2023, 11:15 PM -
Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome.
Whole Transcriptome RNA-seq
Whole transcriptome sequencing...08-31-2023, 11:07 AM
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