Question: What tools / datasets for long-reads mapping benchmarking ? (MinION or PacBIO)
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gravatar for Tintest
2.0 years ago by
Tintest0
France
Tintest0 wrote:

Hello everyone,

I often come to glean answers here, today I take the plunge, I subscribe to ask my first question! I will soon be working with RNA long-reads, and I'd like to do some preliminary testing before concentrating on MinION technology.

Before starting, I wanted to make a stock of tools and datasets to be able to test the tools and compare them. Unfortunately, I am much familiar with the DNA-seq that I am with the RNA-seq. I do not know what datasets I can find / use, something that can be used as a control for benchmarking as can be NA12878 in genomics. Do you know anything that I could have missed ?

I have the impression that there is not much human data in RNA-seq MinION, I am not refractory to turn to PacBio, where there is data. I saw that the community generally used GMAP, STAR to align against a genome of PacBio or BLASR reads against known transcripts. But like previously, I don’t really know what data to use to test if my tools are the right ones.

Thank you !

ADD COMMENTlink written 2.0 years ago by Tintest0

I have the impression that there is not much human data in RNA-seq MinION

I have the impression that you are right about this.

ADD REPLYlink written 2.0 years ago by WouterDeCoster37k

Well it's already good to know. Thank you !

ADD REPLYlink written 2.0 years ago by Tintest0
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