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Old 04-04-2016, 08:19 AM   #1
abmenezes
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Location: Canberra, Australia

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Default MEGAN: impact of max number of hits in read annotation

Hi all,

I am a MEGAN user and I am deciding on thresholds to use for the annotation of metagenomic reads. I performed a test, blasting (using last+) the same sequence dataset using the same evalue, but different maximum number of maximum hits. Increasing the number of blastx hits from 2 to 10 led to a decrease (by about half) in the number summarized reads for each taxa.
Does anyone know why that would happen?
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Old 07-20-2016, 07:47 AM   #2
bastianwur
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Normally then the number of unassigned reads should increase (because the assignment gets too fuzzy).
If not...where did they go to?
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