Is it possible to convert 3 prime sequencing read counts into TPMs?
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9 months ago
Mat ▴ 60

I have got read counts from 3 prime sequencing and would like to make a rough comparison with other RNAseq dataset for which have got transcripts per million (TPM) values. Is it possible to convert the read counts into TPMs as well?

Steps to calculate TPM from read counts (taken from https://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/):

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

Steps 2 and 3 seem to be clear. However, I don't know what to do in step 1 since it is not full length sequencing. What factor should I use there or can I just skip it?

Thanks a lot for your help.

RNAseq TPM expression • 511 views
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9 months ago
Trivas ★ 1.8k

No, since 3' end sequencing is basically counting individual transcript abundances. You could probably get away with dividing the counts per gene by the total number of gene counts and get a similar enough value to TPM.

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Thanks. When I convert them to CPM (norm by library size and 1M scaling factor) it looks good enough for a rough comparison.

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