[BUG] After running filter, the second column of the filtered gtf file is always `pacbio`, even if I'm using ONT data.

[dudududu12138]

Is there an existing issue for this?

• [X] I have searched the existing issues

Have you loaded the SQANTI3.env conda environment?

• [X] I have loaded the SQANTI3.env conda environment

Problem description

After running sqanti3_qc.py and sqanti3_filter.py, I got a filtered.gtf, but the second column of the gtf file is always PacBio. My input data is ONT data. Below is my output:

GL000194.1      PacBio  transcript      53589   115018  .       -       .       transcript_id "TCONS_00000129"; gene_id "XLOC_000075";
GL000194.1      PacBio  exon    53589   55676   .       -       .       transcript_id "TCONS_00000129"; gene_id "XLOC_000075";
GL000194.1      PacBio  exon    112792  112850  .       -       .       transcript_id "TCONS_00000129"; gene_id "XLOC_000075";
GL000194.1      PacBio  exon    114986  115018  .       -       .       transcript_id "TCONS_00000129"; gene_id "XLOC_000075";
GL000219.1      PacBio  transcript      77559   99699   .       -       .       transcript_id "TCONS_00000829"; gene_id "XLOC_000183";
GL000219.1      PacBio  exon    77559   78952   .       -       .       transcript_id "TCONS_00000829"; gene_id "XLOC_000183";
GL000219.1      PacBio  exon    79937   80028   .       -       .       transcript_id "TCONS_00000829"; gene_id "XLOC_000183";
GL000219.1      PacBio  exon    83213   83317   .       -       .       transcript_id "TCONS_00000829"; gene_id "XLOC_000183";

Code sample

module load miniconda3
source activate SQANTI3.env

sample=$1
echo -e "$sample"

ref_anno=~/reference/merge/merge.combined.gtf
ref=~/reference/GRCh38.p14.genome.fa
polyA=~/software/SQANTI3-5.2.1/data/polyA_motifs/mouse_and_human.polyA_motif.txt
cage=~/software/SQANTI3-5.2.1/data/ref_TSS_annotation/human.refTSS_v3.1.hg38.bed

input=$sample.gtf

sqanti3_qc.py $input  $ref_anno  $ref \
        -t 2 -d ./ -o $sample \
        --report skip --force_id_ignore \
        --CAGE_peak $cage --polyA_motif_list $polyA

sqanti3_filter.py rules ${sample}_classification.txt \
 -j filtering.json \
 --isoforms ${sample}_corrected.fasta    \
 --gtf ${sample}_corrected.gtf \
 --faa ${sample}_corrected.faa \
 --skip_report \
 -d $output -o $sample

[aarzalluz]

Hi @dudududu12138 -this is done internally by default, but it does not have any impact in downstream analysis.

Ángeles

[dudududu12138]

Hi @dudududu12138 -this is done internally by default, but it does not have any impact in downstream analysis.

Ángeles

Thanks，I checked your scripts and found the reason. It is indeed as you say.