Output splicing for alignment with gff or gtf

Question

[Bioinf_Questions]

Hello everyone. I need to create a output splicing file for my RNA-seq alignment. However, I only have the gff3 and fasta versions of the genome and according to the script I followed before for other alignments (https://github.com/dekoning-lab/ezmap/blob/master/tools/HISAT2/hisat2-2.0.5-Linux/extract_splice_sites.py) I need a gtf file. I looked for ways to convert gff3 to gtf, but also saw that some problems may arise from this conversion. SO I would like to know if it is possible to create the splicing file with gff3 directly. If not, is AGAT a good tool to convert the file?

Thanks in advance.

Answer 1

[Juke34]

You can try on a subset and see what solution works best for you: https://agat.readthedocs.io/en/latest/tools/agat_convert_sp_gff2gtf.html

Answer 2

[benformatics]

Convertion Of Gff3 To Gtf

Converting GFF to GTF