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Hello, I am very confused, I have RNA-seq data and I have mapped it to my assembled genome (still a few hundred contigs) so I have got about 20000 mapped contigs. My question is how can I translate that into transcripts? I mean how can I know two or more contigs belong to the same transcript. Is it possible to know how many genes do I have? Can I use that information to annotate my genome? I have annotated it with predictions and I was expecting to keep only the predictions that I have evidence for in my RNA-seq data but I don't know how to do that. How to make that link? Any help will be very much appreciated, thanks.
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...