Can the latest gtf file be used as the annotation file with the old reference genome available in galaxy?

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Hi, I am performing reference based RNA-Seq.
In that I am using mm10 (MusMusculus10) as my reference genome and want to use GRCm39.111.gtf.gz as the annotation file. Will it be compatible?

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Hi @Sanjukta_Ghosh
generally, the answer is No. There are some exceptions when genome coordinates stay the same, but these exceptions are (extremely) rare. Data must be from the same version of a genome assembly.
Either use annotation for mm10, or import GRCm39 genome assembly (fasta file) into your history, and during setup of alignment job (with HiSAT2 or similar tool) change Source of reference genome from Built-in to In History. The BAM file will be compatible with GRCm39 annotation.
Kind regards,
Igor

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