stringtie recognizes and converts CDS?

[choiseungji]

In order to confirm the error of the splicing function due to the mutation, it is necessary to check the existence of the intron. I wanted to quantify the intron by deleting all the CDS part from the gff file and changing it to CDS by putting intron information.

ID=YCL005W-A is a gene with two introns. but , command stringtie -e -B -p 20 -G CDS_conversion_only_intron.gff -o ballogwn/ulp2_50G_1/ulp2_50G_1.ballgown.gtf -A ulp2_50G_1/gene_abund.tab /home/jc2545/scratch60/ulp2/ulp2_50G_1/ulp2_50G_1.MAPQ10.hisat2.bam

The intron cov comes out as 0, and another line of the same gene with the source column as stringtie is created below it, and there is also a cov, but the intron positions are changed for some reason.

Can you tell me how stringtie recognizes and converts CDS? Also, if there is another good way to quantify introns, please let me know.

The first attachment is the input file that converted intron to CDS, The second attachment is the output file

Thank you :

[choiseungji]

I tried modifying the frame and attributes columns, but there was no difference.