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I am trying to build a HISAT2 index using Pertea et al. procedure (https://www.ncbi.nlm.nih.gov/pubmed/27560171) using their extract_splice_sites.py and extract_exons.py pieces of code. For that, I need a .gtf file of Human Genome HG38. I have obtained this file using recommendations described here http://www.metagenomics.wiki/tools/fastq/ncbi-ftp-genome-download

The file I have downloaded is GCF_000001405.39_GRCh38.p13_genomic.gff (1,1 Gb) and when I use on it this command python3 extract_splice_sites.py GCF_000001405.39_GRCh38.p13_genomic.gff > test.ss my test.ss file is 0 Kb! I wonder if there's another .gff file that I must use and where I can get it? This is my first time working with the human genome so I am not sure if I am doing the procedure the right way.

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You can download a GTF file from NCBI now. For hg38 (also known as GRCh38), just go to NCBI Assembly and search for 'GRCh38'. Click on the first result to go to this page and use the blue 'Download Assemblies' button to download data. Here, after you choose 'RefSeq' as your source of data, you will see a GTF file to download from the drop-down list, as shown in the screenshot below: enter image description here

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I had the same problem and I was able to solve it with that https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gff_to_gtf.md

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