Fastq Screen shows many unmapped reads

Question

[esimonova.me]

I performed fastq_screen analysis of human tumor samples and it looks like that either READ1 or READ2 show high number of unmapped reads. I received the data from a vendor and I try to figure out what causes this behavior?

[Pierre Lindenbaum]

check the qualities of the reads (poly-NNN ?) , pick a few unmapped reads and run NCBI blast.

[esimonova.me]

Poly-N content is fine, no N were called . I will pick them in the next step as fastq_screen doesnt generate BAM files