Hi everyone. I’m working with NGS data from human cells infected with a virus, so my FASTQ files contain both host and viral DNA reads.
My goal is accurate peak calling on both host and viral genomes, and I want to avoid mis-mapping or losing viral reads.
For alignment, is it better practice to:
build a combined reference genome and align once, or align to human first and then map unmapped reads to the viral genome separately? do you have a better idea?
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written
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hajar •
In case it's a retro-virus, you might want to check if there are viral sequences/traces in the human reference and mask these sequences before combining the two genomes.
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