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ConesaLab / SQANTI3

Tool for the Quality Control of Long-Read Defined Transcriptomes
GNU General Public License v3.0
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Missclassification of Genic Intron transcripts #315

Closed liniguez closed 3 months ago

liniguez commented 4 months ago

Is there an existing issue for this?

Have you loaded the SQANTI3.env conda environment?

Problem description

I created a gtf to understand the classification of transcripts and this is a summary of the outcome:

Classification

For all of the categories the classification is as expected but the genic intron ones are classified as intergenic. I guess this is a bug in the code.

I used the reference you are providing of in the example folder and the gtf from the tested transcripts is the folloing:

chr22 PacBio transcript 35540000 35540731 . + . gene_id "PB.123"; transcript_id "PB.123.1"; chr22 PacBio exon 35540000 35540731 . + . gene_id "PB.123"; transcript_id "PB.123.1"; chr22 PacBio transcript 35540831 35553999 . + . gene_id "PB.123"; transcript_id "PB.123.2"; chr22 PacBio exon 35540831 35541500 . + . gene_id "PB.123"; transcript_id "PB.123.2"; chr22 PacBio exon 35546801 35547080 . + . gene_id "PB.123"; transcript_id "PB.123.2"; chr22 PacBio exon 35551503 35553999 . + . gene_id "PB.123"; transcript_id "PB.123.2"; chr22 PacBio transcript 35540831 35553999 . - . gene_id "PB.123"; transcript_id "PB.123.3"; chr22 PacBio exon 35540831 35541500 . - . gene_id "PB.123"; transcript_id "PB.123.3"; chr22 PacBio exon 35546801 35547080 . - . gene_id "PB.123"; transcript_id "PB.123.3"; chr22 PacBio exon 35551503 35553999 . - . gene_id "PB.123"; transcript_id "PB.123.3"; chr22 PacBio transcript 35540831 35553999 . + . gene_id "PB.123"; transcript_id "PB.123.4"; chr22 PacBio exon 35540831 35541500 . + . gene_id "PB.123"; transcript_id "PB.123.4"; chr22 PacBio exon 35551503 35553999 . + . gene_id "PB.123"; transcript_id "PB.123.4"; chr22 PacBio transcript 35540831 35553999 . + . gene_id "PB.123"; transcript_id "PB.123.5"; chr22 PacBio exon 35540831 35541500 . + . gene_id "PB.123"; transcript_id "PB.123.5"; chr22 PacBio exon 35543258 35543458 . + . gene_id "PB.123"; transcript_id "PB.123.5"; chr22 PacBio exon 35548932 35549286 . + . gene_id "PB.123"; transcript_id "PB.123.5"; chr22 PacBio exon 35551503 35553999 . + . gene_id "PB.123"; transcript_id "PB.123.5"; chr22 PacBio transcript 35540931 35553899 . + . gene_id "PB.123"; transcript_id "PB.123.6"; chr22 PacBio exon 35540931 35541500 . + . gene_id "PB.123"; transcript_id "PB.123.6"; chr22 PacBio exon 35551503 35553899 . + . gene_id "PB.123"; transcript_id "PB.123.6"; chr22 PacBio transcript 35546700 35547480 . + . gene_id "PB.123"; transcript_id "PB.123.7"; chr22 PacBio exon 35546700 35547480 . + . gene_id "PB.123"; transcript_id "PB.123.7"; chr22 PacBio transcript 35546700 35547480 . - . gene_id "PB.123"; transcript_id "PB.123.8"; chr22 PacBio exon 35546700 35547480 . - . gene_id "PB.123"; transcript_id "PB.123.8"; chr22 PacBio transcript 35546851 35553999 . + . gene_id "PB.123"; transcript_id "PB.123.9"; chr22 PacBio exon 35546881 35547080 . + . gene_id "PB.123"; transcript_id "PB.123.9"; chr22 PacBio exon 35551503 35553999 . + . gene_id "PB.123"; transcript_id "PB.123.9"; chr22 PacBio transcript 35546891 35547280 . + . gene_id "PB.123"; transcript_id "PB.123.10"; chr22 PacBio exon 35546891 35547280 . + . gene_id "PB.123"; transcript_id "PB.123.10"; chr22 PacBio transcript 35546891 35547280 . - . gene_id "PB.123"; transcript_id "PB.123.11"; chr22 PacBio exon 35546891 35547280 . - . gene_id "PB.123"; transcript_id "PB.123.11"; chr22 PacBio transcript 35548068 35548968 . + . gene_id "PB.123"; transcript_id "PB.123.12"; chr22 PacBio exon 35548068 35548968 . + . gene_id "PB.123"; transcript_id "PB.123.12"; chr22 PacBio transcript 35548068 35548968 . - . gene_id "PB.123"; transcript_id "PB.123.13"; chr22 PacBio exon 35548068 35548968 . - . gene_id "PB.123"; transcript_id "PB.123.13"; chr22 PacBio transcript 35547580 35550100 . + . gene_id "PB.123"; transcript_id "PB.123.14"; chr22 PacBio exon 35547580 35547980 . + . gene_id "PB.123"; transcript_id "PB.123.14"; chr22 PacBio exon 35549980 35550100 . + . gene_id "PB.123"; transcript_id "PB.123.14"; chr22 PacBio transcript 35540831 35553999 . + . gene_id "PB.123"; transcript_id "PB.123.15"; chr22 PacBio exon 35540831 35541500 . + . gene_id "PB.123"; transcript_id "PB.123.15"; chr22 PacBio exon 35546801 35553999 . + . gene_id "PB.123"; transcript_id "PB.123.15"; chr22 PacBio transcript 35540800 35554500 . - . gene_id "PB.123"; transcript_id "PB.123.16"; chr22 PacBio exon 35540800 35554500 . - . gene_id "PB.123"; transcript_id "PB.123.16";

carolinamonzo commented 3 months ago

Hi, Thanks for using SQANTI3! This issue is solved in the newest release v5.2.2. Please update your SQANTI3 installation with the newest release.

Best wishes!