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Hi, I used the PRAM pipeline to predict the intergenic transcripts including 300 plant samples transcipts data. There are
20,313 transcript models grouped into 12,019 gene models. Then I added this intergenic gtf into my genome anottation gtf to quantified each samples' gene TPM by using STAR to align reads and Stringtie to calculate the value of TPM. After that, I found there are 5,000 novel intergenic transcripts got 0 TPM in any samples. I checked the data that you quantified in isoforms.tpm.gz. It is also have nearly 900 novel intergenic transcripts got 0 TPM in any samples. But it is much better than me.
I want to ask why PRAM pipeline produce these 0 TPM intergenic transcripts. And, How you quantified your intergenic transcipts? My results looked uncredible.
Thank you very much.