Question: GTF/GFF3 file compatible with (GRCh38/hg38)(hg38)
0
gravatar for kanwarjag
5 months ago by
kanwarjag1.1k
United States
kanwarjag1.1k wrote:

I am using Reference genome -Human Dec2013 (GRCh38/hg38)(hg38) and gene model Homo_sapiens.GRCh38.101.gff3.gz however I get error saying chromosome naming is not matching. I know that Ensembel uses Chr as prefix. The question is if I use Human Dec2013 (GRCh38/hg38)(hg38) as reference assembly, which gene model file of hg38 should be compatible without editing gene model gtf or gff3 file and from where I can download? Will Gencode GRCh38 GTF file be compatible with Human Dec2013 (GRCh38/hg38)(hg38)? Thanks

rna-seq • 359 views
ADD COMMENTlink written 5 months ago by kanwarjag1.1k

Is the reference genome from NCBI..? If yes, NCBI also provides gff.

ADD REPLYlink written 5 months ago by AISHA120

I would download everything again from the same source and learn to always check chr names in a text editor before using.

I recommend ENSEMBL and GenCode for good, consistent resources. I have had better experiences there than with NCBI or UCSC efforts.

ADD REPLYlink written 5 months ago by colindaven2.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1417 users visited in the last hour
_