I have a dataset where some of the samples has been sequenced with
Illumina Genome Analyser II, some with
Illumina Genome Analyser IIx and the rest with
Illumina Hiseq 2000. Now, I know that, I can run sequences from Genome analyser II and Hiseq 2000 with MetaPhlAn and HUMAnN, but not sure about the output from Genome analyser IIx. Can I run MetaPhlAn and HUMAnN with the sequence coming from Illumina Genome Analyser IIx platform?
Also, should I compare the relative abundances of the features (taxa and pathways) coming from
Genome Analyser IIx Vs Hiseq2000 to find out differentially abundant taxa?
I mean, I am confused if it is suitable to compare sequences coming from different platforms.