Deleting human reads on MEGAN deskptop

User Questions
1

Hello,

I have a metagenomic sample in MEGAN6. I tried to filter my sample to get rid of human reads in command line before uploading into MEGAN6, but there are some still remaining.

Is there a way to delete reads from a specific family or genus on MEGAN6, if so how do I do this?

Thank you,
Alima

2

You can specify one or more contaminant taxa in a file (one per line) and then upload this file during meganization. Then any read that has any significant alignment against the taxon (or to any of its descendants) will be placed on a special “Contamination” node.

3

Thanks for the reply! Thats super helpful