GTF/GFF3 file compatible with (GRCh38/hg38)(hg38)
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22 months ago
kanwarjag ★ 1.2k

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 • 1.1k views
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Is the reference genome from NCBI..? If yes, NCBI also provides gff.

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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.

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