I've installed BLAST and BLAT on my computer (OSX) but am confused with how many different files there are to download to set up a database on my computer and how to go about it. Can I use one with both BLAST and BLAT? Should I get the partially non-redundant database?
Once you have installed `blat`, you can download a FASTA file for your genome of interest from UCSC. If you wanted `hg38`, for instance:

    $ for chr in `seq 1 22` X Y; do echo $chr; wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg38/chromosomes/chr$chr.fa.gz | gunzip -c - >> hg38.fa; done

You can use this with `blat` as described in [my answer here][1].

You could run `makeblastdb` to [make BLAST databases][2]:

    $ makeblastdb -in hg38.fa -parse_seqids -dbtype nucl

Or [download nucleotide databases from NCBI][3].


  [1]: https://www.biostars.org/p/261839/#261983
  [2]: https://www.ncbi.nlm.nih.gov/books/NBK279688/
  [3]: ftp://ftp.ncbi.nlm.nih.gov/blast/documents/blastdb.html