hg38 Ensembl GTF file

Question

[Gregor Rot]

Dear all, what is the difference between the hg38 Ensembl GTF file:

ftp://ftp.ensembl.org/pub/release-90/gtf/homo_sapiens/Homo_sapiens.GRCh38.90.gtf.gz

and

ftp://ftp.ensembl.org/pub/release-90/gtf/homo_sapiens/Homo_sapiens.GRCh38.90.chr.gtf.gz

(note the .chr. addition in the name)

Thank you, Gregor

Answer 1

[Emily]

GRCh38.90.gtf.gz contains everything including unplaced scaffolds. GRCh38.90.chr.gtf.gz contains only the stuff on properly assembled chromosomes.

[Gregor Rot]

Thank you Emily, looking at the files, the number of lines is almost identical: 2612848 lines for gtf, 2612134 for .chr.gtf. Also from your answer, you perhaps mistyped and wrote the same name for both files. I assume the .chr.gtf is the one on "properly assembled chromosomes"? Thanks again

[Emily]

Yes, mistyped. Will fix the answer.

800 lines sounds about right. Human doesn't have many unplaced scaffolds.