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/):
- 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. 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.