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stat quest stat quest stat quest hello and welcome to stat quest stat quest is brought to you by the friendly folks in the genetics department at the University of North Carolina at Chapel Hill today were going to be talking about rpkm versus fpkm versus fpm in previous stat quests weve talked about topics that are broadly applicable to a variety of fields these subjects however really only relate to high-throughput sequencing of RNA so if thats what youre interested in quest on theres a new RNA seek metric on the block we used to report rpkm or reads per kilobase million or fpkm fragments per kilobase million these normalized read counts for the sequencing depth thats the million part because sequencing runs with more depth will have more reads mapping to each gene that in sequencing runs with less depth and we dont want that to bias our analysis the other thing that these metrics normalized for are the lengths of genes thats the kilobase part longer genes will naturally have

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What is the size of the human transcriptome?

The 600 Gb is produced in the form of 6 billion short reads, each approximately 100 bp in length (using the Illumina HiSeq sequencer), and assembling these reads into chromosomes is a very complex, highly specialized task.

What is the size of the human reference genome?

Results. The male nuclear diploid genome extends for 6.27 Gigabase pairs (Gbp), is 205.00 cm (cm) long and weighs 6.41 picograms (pg). Female values are 6.37 Gbp, 208.23 cm, 6.51 pg.

How many transcripts does human transcriptome have?

Although there are fewer than 22,000 protein coding genes known in the human genome, they are transcribed into over 140,000 different transcripts (Ensembl release 66 [1]), over 65% of which have protein coding potential and thus may contribute to protein diversity.

What is the average transcript length of a human?

For example, the average transcript lengths of eukaryotic genes range from 1108 to 2667 bp in human and from 1135 to 1695 bp in yeast [54] .

What is TPM vs CPM?

CPM is basically depth-normalized counts, whereas TPM is length-normalized (and then normalized by the length-normalized values of the other genes). If one has to choose between those two choices one typically chooses TPM for most things, since generally the length normalization is handy.

How much of the human genome can be transcribed?

And many bases are simply places where chemical modifications serve to silence stretches of our chromosomes. ENCODEs results are changing how scientists think about genes. It found about 76% of the genomes DNA is transcribed into RNA of one sort or another, way more than researchers had originally expected.

How to calculate TPM?

Heres how you calculate TPM: Divide the read counts by the length of each gene in kilobases. This gives you reads per kilobase (RPK). Count up all the RPK values in a sample and divide this number by 1,000,000. This is your per million scaling factor. Divide the RPK values by the per million scaling factor.

What does TPM mean in RNA-seq?

Therefore, RNA-seq isoform quantification software summarize transcript expression levels either as TPM (transcript per million), RPKM (reads per kilobase of transcript per million reads mapped), or FPKM (fragments per kilobase of transcript per million reads mapped); all three measures account for sequencing depth and

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