mapping gtf version different with TEtranscripts version

[songlyzz]

Hi olivertam， I I'd like to ask for advice that I use gencode v25 gtf to map, the version is different with GRCh38_Ensembl_rmsk_TE.gtf. Will it still work well in different reference version?

Thanks, Song

[olivertam]

Hi Song,

Thank you for your interest in the software.

I'm assuming you're using GENCODE FASTA for mapping, and the GENCODE v25 GTF for gene annotation. I would recommend using GRCh38_GENCODE_rmsk_TE.gtf, which uses the same chromosome nomenclature as GENCODE.

Unfortunately, a mismatch in chromosome nomenclature will result in no annotation for those features, so it's highly recommended to use annotations and FASTA with the same chromosome names.

Thanks.

[songlyzz]

Thank you very much!

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