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Could someone help me understand what the difference between transcript and primary transcript on phytozme is? For example, this dataset of A.thaliana has "primary transcript CDS" vs CDS.

Off the top of my head primary transcript represents the initial strand of RNA made from DNA and transcripts represent genes post-processing of the initial strand.

The thing that is confusing me is, why is the transcript file larger than the primary transcript file? The transcript file has about 21k more headers than the "primary transcript". The only explanation I can think of is that due to alternate splicing you could end up with a bunch of isoforms that lend more headers to the transcript file. Is that it?

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According to a team lead at Phytozome:

Multi-exon genes can produce different transcripts via process of alternative splicing:  inclusion/exclusion of particular exons in the spliced transcript.Designation of one of these transcripts as “primary” will vary based on the genome under consideration:  the primary might be the one with the highest expression under “normal” conditions, it might be the one whose mutations was first studied, or it might simply be the transcript with the longest CDS.

In all cases, Number_of_transcripts >= Number_of_primary_transcripts                    Number_of_primary_transcripts == Number_of_genes

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