Sqanti rescue: introducing duplicate transcripts in the gtf file

[ChrissiKalk97]

Hi everyone,

I found that some transcripts appear twice in the gtf file I obtain after the Sqanti rescue step (I used a custom rules filter for the Sqanti filter step and ran the rescue step in the full mode):

`/scratch/fuchs/agschulz/kalk/Squanti3/final_assembly_rescue_06_12_24
grep 'ENST00000674426' rescue_custom_rules_filter_rescued.gtf
1 PacBio transcript 35883228 35930531 . + . transcript_id "ENST00000674426"; gene_id "ENSG00000092847";
1 PacBio exon 35883228 35883446 . + . transcript_id "ENST00000674426"; gene_id "ENSG00000092847";
1 PacBio exon 35888427 35888610 . + . transcript_id "ENST00000674426"; gene_id "ENSG00000092847";
...

1 havana transcript 35883209 35930532 . + . transcript_id "ENST00000674426"; gene_id "ENSG00000092847"; gene_name "AGO1"
1 havana exon 35883209 35883446 . + . transcript_id "ENST00000674426"; gene_id "ENSG00000092847"; gene_name "AGO1";
1 havana exon 35888427 35888610 . + . transcript_id "ENST00000674426"; gene_id "ENSG00000092847"; gene_name "AGO1";
...
1 havana CDS 35883422 35883446 . + 0 transcript_id "ENST00000674426"; gene_id "ENSG00000092847"; gene_name "AGO1";
1 havana CDS 35888427 35888610 . + 2 transcript_id "ENST00000674426"; gene_id
...`
For the gtf file of the QC and the filter step the same transcript ID was present but only as one transcript, so the duplication occurred somewhere in the rescue procedure.

If anyone knows why this happens or how to circumvent this, I would much appreciate you sharing your knowledge and experience :)

Best,

Christina