I am a little bit confused on which human genome assembly and annotation to use.
First issue I would like to use Ensembl assembly and annotation. My doubts are: if i use the latest release (v74) i tend to use the "primary assembly" which doesn't contain patches (ftp://ftp.ensembl.org/pub/release-74/fasta/homo_sapiens/dna/). I do that because to my knowledge fix patches provide duplicate chromosomal sequence and when i would be mapping my reads i would get multiple hits in these patched regions (since the patches are provided in separate N-padded files). Maybe i am wrong here?
Second issue When i download the annotation over biomart (v74), i get genes on patched chromosomes (an example is SLC25A26 : http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000261657). I don't want to loose these genes (since there are no patched chromosomes in the primary assembly).
Is there a way to get the latest patched human genome assembly sequence (with patches already applied to the genomic sequence, and not in separate files)? Thanks