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

[diekhans]

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?

This depends on your needs. We tend to use GENCODE, it is more comprehensive RefSeq, however it has more transcript that are of unknown function. GENCODE most agree with RefSeq on the well characterized transcripts. For the purposed of long-read isoforms classification, more annotations are generally useful.

Although we highly recommend

• 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?

GENCODE, Ensembl, and UCSC are the same gene models, however, for historic reasons, they use different names for the chromosomes. If believe GENCODE from https://www.gencodegenes.org/ will match.

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?

Highly suitable

[Alina-Song]

Thank you so much for the quick and detailed response! This clears up my confusion perfectly. Really appreciate your help!