8. RNA-sequence Analysis: Expression, Isoforms

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MIT 7.91J Foundations of Computational and Systems Biology, Spring 2014
Instructor: David Gifford

This lecture by Prof. David Gifford is about RNA-seq (RNA sequencing), a method of characterizing RNA molecules through next-generation sequencing. He begins with the principles of RNA-seq, and then moves on to how to analyze the data generated by RNA-seq.

License: Creative Commons BY-NC-SA

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The number of isoforms should be (2^n) - (1) and not 2^n (as mentioned at 26:25). Every exon has 2 possibilities and one is subtracted because there is also a state where no exon is present.

notAnon

This video is very interesting. Makes it very easy to understand how RNA-Seq platform works

lakeshed

It's not easy to understand this complicated stuff, but your explanation is really helpful for me to be clear about it. Thank you very much!

songthanh

great explanation of the hypergeometric test. finally got it

wimthiels

the Prof said that in DESeq, Sj is estimated based on each condition separately, but the paper only shows that the variance is estimated that way, not the size factor. Also, I dont think it is necessary to estimate the sequencing depth factor within conditions only. This would make the calculation of fold change impossible, since the mu for each gene is on a different scale.

kyang

56:20 principal component analysis PCA

sfmambero

38:26 what’s the rationale for chi-squared distribution to answer the original modeling? It sounds like the probability is only dependent on the number of parameters and the quality of modeling. Or, in other words, why can we use it for any H0 and H1?

nowayyesway

Object modeling is a fundamental tool for analyzing and expressing data requirements. Which aspects seem easiest and most difficult for you?

akathebest

Interesting talk. I have a query that Is it possible to predict bacterial transcription start sites (TSS) using RNA-Seq ??

ainala

If there is n no of exon, there there could be 2^n -1 isoform?
Suppose for 3 exon a, b, c . The Exons are a, b, c, ab, ac, bc, abc .so total 7 isoform not 8

koustavroy

this is 9 years old, do you have plans to update it?

George-rqyp

Anyone know how come when one particular sample had twice as many reads as the other, the scaling factor would be two? Though it would be square root 2 or something

jadecheng

50:00 "The mean value theorem" lol

alcyonecrucis

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