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COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
https://combine-lab.github.io/salmon
GNU General Public License v3.0
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Opinion on --posBias #474

Open PlantDr430 opened 4 years ago

PlantDr430 commented 4 years ago

Just wanted to put an opinion in. I am currently using Salmon v1.1.0 and noticed that --posBias wasn't listed in the help messages, but I found it in your read the docs. I tested it out and it made a significant improvement in my calculations. I know it is considered "experimental", but it helped in my research and will publish that I used it when we get the manuscript out.

Also, do you think you could give a brief explanation on what --forgettingFactor is doing and how it could be affecting quantification calculations?

regelka commented 4 years ago

In Salmon v1.2.0, --posBias is listed in the help message without any hints on being "experimental". At the same time, the read the docs manual still lists it as an experimental feature.

Does someone know if it is now considered as a stable feature?