Question: hg38 Ensembl GTF file
0
gravatar for Gregor Rot
2.1 years ago by
Gregor Rot440
Zurich, Switzerland
Gregor Rot440 wrote:

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

hg38 ensembl gtf • 2.3k views
ADD COMMENTlink modified 2.1 years ago by Emily_Ensembl20k • written 2.1 years ago by Gregor Rot440
4
gravatar for Emily_Ensembl
2.1 years ago by
Emily_Ensembl20k
EMBL-EBI
Emily_Ensembl20k wrote:

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

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Emily_Ensembl20k

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

ADD REPLYlink written 2.1 years ago by Gregor Rot440
1

Yes, mistyped. Will fix the answer.

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

ADD REPLYlink written 2.1 years ago by Emily_Ensembl20k
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