I have some RNA sequencing reads to align to the human reference genome. I found the genome FASTA files on both [GENCODE][1] and [ENSEMBL][2]: `GRCh38.p13.genome.fa.gz` and `Homo_sapiens.GRCh38.dna.toplevel.fa.gz` 
But after unzipping them, I found that they are 3.1G and 60G respectively. Why is that? And which one should I use? (considering the purpose of the project is to detect gene fusion from the sequencing reads).


  [1]: http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/
  [2]: http://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/dna/
`toplevel` file from Ensembl includes haplotypes with full length of chromosome padded out using N's. That is the reason it is huge compared to GENCODE file. Use the Ensembl primary file which is equivalent to GENCODE.

From README at Ensembl:


    ---------
    TOPLEVEL
    ---------
    These files contains all sequence regions flagged as toplevel in an Ensembl
    schema. This includes chromsomes, regions not assembled into chromosomes and
    N padded haplotype/patch regions.