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2 hours ago by

I made single-cell ATAC-seq libraries from human brain, but I am getting upto 70% reads unmapped to human, these unmapped reads seem to have highest hit to bacteria. Can someone please suggest how to reduce bacterial contamination in ATAC-seq? Could these be multi-mapping reads, and how could I remove them from fastq files? Does sequencing to 10x more depth than recommended cause bacteria reads to occur if library complexity is low?
Thank you!

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C40



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