Скачать или смотреть RNA-Seq Rescue Algorithm Part 2 of 2

RNA-Seq Rescue Algorithm: Please note that the full RSEM algorithm is too complicated to execute manually. Nonetheless, we can use the RNA-Seq rescue method to approximate 1 iteration of Expectation-Maximization. Please note that in this video, Saniya will work on an example of a bipartite graph (a graph whose vertices can be divided into two disjoint and independent sets U and V, that is every edge connects a vertex in U to one in V), which has 2 types of nodes: transcripts (with RNA base pair lengths) on the left hand side and read groups on the right hand side.

1.) The transcript nodes contain a transcript ID and the transcript length is in base pairs (bp).

2.) The read nodes contain the read counts for a group of reads that all align to the same transcripts.

Here, the edges designate the transcripts that each read group aligns to.

Please note that this video is a continuation of the example in Part 1 (   • RNA-Seq Rescue Algorithm Part 2 of 2  ), where Saniya used the RNA-Seq rescue method to calculate the relative abundances for 5 RNA transcripts (Transcript 1, 2, 3, 4, and X). In this vide, Saniya explains the concepts of RNA Spike-Ins like Transcript X (that is 100 base pairs), and shows how Spike-Ins can be used to find the absolute abundances for the other 4 RNA transcripts (1, 2, 3, and 4).

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