Question about no_feature count in transcript_model_counts.tsv

[FabianJetzinger]

Hello!

I'm trying to understand the output of IsoQuant in more detail, specifically .transcript_counts.tsv and .transcript_model_counts.tsv, using the toy data (MAPT.Mouse) from this repository.

Running:
isoquant.py --reference MAPT.Mouse.reference.fasta --genedb MAPT.Mouse.genedb.gtf --fastq MAPT.Mouse.ONT.simulated.fastq --data_type nanopore -o toy_data_out

While there are 12 Transcripts in the OUT.transcript_counts.tsv, there are only 10 in OUT.transcript_models.tsv; I take this to mean that for the two transcripts "ENSMUST00000100347.10" and "ENSMUST00000146353.1", IsoQuant does not see enough evidence in the reads to include their transcript models, even though they are known reference transcripts. This seems to be supported by the fact that OUT.read_assignments.tsv shows no FSMs for these two transcripts, only ISMs.

What confuses me, however, is that OUT.transcript_counts.tsv shows "no_feature 15", while OUT.transcript_model_counts.tsv shows "no_feature 0", where I would have expected either "no_feature 15" (the same 15 completely unassigned reads), or even "no_feature X" (where X is the 15 unassigned reads, plus the number of reads assigned to the transcripts which were not included in the transcript_models).

See isoquant_OUT.zip

What am I missing or misunderstanding here? Is this number just always 0 for the transcript_model? Sadly I wasn't able to come up with an answer from reading older issues, so any help would be greatly appreciated.

[andrewprzh]

Dear @FabianJetzinger

Sorry for the delayed response.

Yes, you are right, inconsistencies between OUT.transcript_counts.tsv and OUT.transcript_models.tsv are normal since they have different nature and underlying algorithms. However, there are known minor flaws and currently I'm working on making them more consistent with each other.

With respect to no_feature attribute, you are also right, it seems that this field is simply ignored in OUT.transcript_models.tsv.
I will fix that, thanks for the report!

Best
Andrey

[FabianJetzinger]

Thanks for your reply, that makes it much clearer!

[andrewprzh]

Should be now fixed in IsoQuant 3.4.

Also, correlation between transcript_model_counts and transcript_counts is better now.