Fastq Screen shows many unmapped reads
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?
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check the qualities of the reads (poly-NNN ?) , pick a few unmapped reads and run NCBI blast.
Poly-N content is fine, no N were called . I will pick them in the next step as fastq_screen doesnt generate BAM files