Missclassification of Genic Intron transcripts

Question

Missclassification of Genic Intron transcripts

Closed this issue 5 months ago · 1 comments

liniguez commented 5 months ago

Is there an existing issue for this?

I have searched the existing issues

Have you loaded the SQANTI3.env conda environment?

I have 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:

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";

Answer 1 · 2024-07-31T08:37:29.000Z

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!