Thank you very much. I get it from UCSC.
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heureuse •
Differences in GTF files hg19 and hg38
Hello,
I have a script for gene annotation with hg19. Now I'm trying to annotate using hg38. The problem is I need the column level (level 1, level 2). I can't find it in the gtf file hg38.
Do you have any idea ?
Thank you
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1 answer
Not sure where you got your GTF for GRCh38 from but one from GENCODE has the level info you are looking for.
chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000290825.1"; gene_type "lncRNA"; gene_name "DDX11L2"; level 2; tag "overlaps_pseud
ogene";
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Thank you very much. I get it from UCSC.
Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have been under. Use
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