Hello, I’m a newbie. I’ve been tried to use MEGAN for my metagenome study, but it quit to hard.
I got 48 sequence data file from environmental samples (feces and soil) for metagenome study using Illumina NextSeq platform(2X150bp, paired-end). After quality filtering and adapter trimming, i got 3 sequence file (Forward, reverse, and single).
Then, i tried several methods before import to MEGAN.
First, 3 sequence files were assembled using metaSPADES. Assembled scaffolds.fasta files were analyzed using DIAMOND for taxonomic assignment. Then from .daa format file, i ran MEGAN using daa2rna.
Second, only forward and reverse sequence files were merged using overlapping merge software FLASH. Then analyzed using DIAMOND for taxonomic assignment. Then from .daa format file, i ran MEGAN using daa2rna.
Actually, i want to see the number of mapped reads like RPKM. But, I’m not sure which is more appropriate and i don’t know how to adapt from MEGAN result.
Dose anyone help which one is best sequence filtering format for MEGAN and how to analyze mapped reads percentage? Thank you.