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.
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Bioinf_Questions •
2 answers
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
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