Recently, I obtained several ChIP-seq data from Saccharomyces Cerevisiae.
After the Illumina sequencing, each fastq contains around ~20 million 50 bp reads. I aligned the reads either with BWA MEM or Bowtie2 to the sacCer3 genome with a very low mapping rate (20% mapped, 80 % unmapped).
I can't figure it out what can cause the unmappability of the reads. Even the input DNA does not align to the genome (50%). I tried to switch genomes but i got always the same overall mapping rate.
What can possibly happened?