Salmon, Getting New TPM from new, updated NumReads
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6.5 years ago
jjrin ▴ 40

Hello, I have recently normalized my read counts (NumReads in Salmon output) and I would like to get the new updated TPMs using these Numreads counts. Is there a method I could go around doing this? The effective length and length would be the same regardless. I have all of the same data available, just with different NumReads now. Knowing how Salmon gets TPM counts would be beneficial as well. Thank you!

salmon Numreads alignment • 2.3k views
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Decent explanation of the units: http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/

R script for conversion:

binary for conversion: https://github.com/mforde84/tpmcalc

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