Very low mapping rate of Hummann v4alpha

Microbial community profiling HUMAnN
1

Hello I tried the new humann 4.0.0a1

Surprisingly I get a very low mapping rate.

The READS_UNMAPPED in the genefamilies represent around 97%.

Ok, I have some pig gut samples where I expect lower mapping rate. but also human control samples, which are public samples. represent <10%.

Is this to be expected?

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2

This would be a very low mapping rate for human microbiome samples. Are you sure they’ve been properly QCed (adapters removed, quality trimmed, and so forth)? That’s a common cause of low mapping rates across the board.