Question: hg38 Ensembl GTF file
0
gravatar for Gregor Rot
17 months ago by
Gregor Rot430
Zurich, Switzerland
Gregor Rot430 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 • 1.4k views
ADD COMMENTlink modified 17 months ago by Emily_Ensembl17k • written 17 months ago by Gregor Rot430
3
gravatar for Emily_Ensembl
17 months ago by
Emily_Ensembl17k
EMBL-EBI
Emily_Ensembl17k 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 17 months ago • written 17 months ago by Emily_Ensembl17k

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 17 months ago by Gregor Rot430
1

Yes, mistyped. Will fix the answer.

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

ADD REPLYlink written 17 months ago by Emily_Ensembl17k
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