How to choose a Genome annotation file

[Alina-Song]

I'm new to bioinformatics analysis and have two basic questions:

1. If I use the recommended reference genome file GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz, how should I choose the corresponding reference genome annotation file?

• Must I download the matched GCF file from NCBI (GCA_000001405.15 → GCF_000001405.26),

• or can I use the latest annotation files from GENCODE, Ensembl, or UCSC instead?

2. For the same samples, we also performed short-read RNA-seq. Is the GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz reference genome suitable for RNA-seq data analysis?

Thank you for your guidance!

[diekhans]

Hi Alina-Song, I am converting this to a discussion and can give you some advice there