Empty TPM counts for transcripts, even when raw counts are present

[Jonas-B-Frank]

Ask away!

I successfully ran the pipeline and am currently looking at the de analysis results (v.1.2.0). I noticed, that not all transcripts, which are listed under unfiltered_transcript_counts_with_genes.tsv also have corresponding TPM counts in unfiltered_tpm_transcript_counts.tsv.
There are some transcripts, which have 0 as TPM (so if the calculation equals to 0, there should be output), and there are some transcripts with TPM counts for only one condition, but not the other (so it cannot only be missing annotation e.g. transcript length). Could you tell me, what the reason for this behaviour might be?
Thank you!

[sarahjeeeze]

Hi, TPM only shows non zero counts - so are the missing ones 0 for all transcripts? If there are counts for one condition it should still show.

[Jonas-B-Frank]

So do I understand it correctly, that if TPM would round down to 0 for all replicates in both conditions, I would get missing values instead of 0s?
Thanks for your help!