Count Output

[Haisuccess93]

Hello, I noticed that in the Isoquant output, there are more gene counts than transcript counts, I mean in terms of number. For example, when I open the Isoquant output for gene counts for one of my data, I have around 16,000 genes with at least 1 count. But for the same sample when I opened the transcript count output, I have around 12,000 transcripts. I think it should be the other way around right? I mean we should have more transcript than we should have genes?
Here is the code I used to quantify the sample
echo "🔄 Processing BP01 with 28 threads..."
isoquant.py --reference /home/ade/ray_organoid/output/Fasta_files/GRCh38.primary_assembly.genome.fa
--genedb /home/ade/ray_organoid/output/Fasta_files/gencode.v47.primary_assembly.annotation.gtf
--fastq /home/ade/ray_organoid/output/Fasta_files/BP01/barcode01.pychopper.fastq
--data_type nanopore --threads 28
-o /home/ade/ray_organoid/output/Fasta_files/BP01/Isoquant
echo "✅ BP01 completed!"

[Haisuccess93]

I used Isoquant 3.6.1

[andrewprzh]

Dear @Haisuccess93

This is normal behavior.

To add a +1 to an isoform abundance, IsoQuant requires a read to be assigned uniquely, meaning that it is consistent with the annotation and there is no ambiguity in the assignment. However, to add +1 to a gene count, a read can be assigned to 2 or more isoforms (of this gene) ambiguously. In other words, not all reads that are unambiguously assigned to a gene can be unambiguously assigned to a transcript. Hence, genes get more counts.

Best
Andrey