Help regarding RNAseq data analysis.

Question

[maverick]

So I am pretty new at this and this may seem a bit naive but can anybody tell me which files do I need to download in order to do the alignment step of the RNAseq data analysis. I am looking to download the .fa and .gtf files of the human reference genome hg38, but I am bit confused as to which file do I need. To clarify, I am a bit lost on which file is the reference genome file and the gtf files. Can anybody provide me a link of the files I would need to download?

Answer 1

[bioinfo_ga]

You can refer to the following links: Genome: ftp://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz GTF: ftp://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.chr.gtf.gz

[maverick]

Thank you so very much for the quick response. However a follow up question to your answer. Do we need the toplevel file or the primary assembly file? I read somewhere that said to avoid downloading the toplevel file and instead go for the primary assembly file.

Answer 2

[igor]

There is a really nice summary of what the different options are as well as what their benefits and drawbacks are available here: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use