ChaoLab
commented
2 years ago Hi Yes, your concern about using the outputs from MEGAN directly as input for METABOLIC is the key. I will not suggest using un-assembled sequences as inputs, especially for your case that you are using metatranscriptomics datasets - which will result in fragmented sequences from microbial genomes. I have used MEGAN before, I think they have a nice, complete pipeline for the whole analysis of short-reads datasets. So sorry it seems incompatible for these two software on a linked analysis.
Hi,
Im very new to bioinformatic and came across this tool recently. I work on metatranscriptomics and i have been following an assembly-free reference based pipeline to get my taxonomic and functional outputs with my data. Right now i have .fasta files (nucleotide) which i obtained after running diamond blast agaist a non-redundant protein database followed my annotation using a tool called MEGAN6. So, i managed to extract out bacterial sequence in .fasta format from MEGAN. Right now, im wondering if i could use those fasta files as an input file with this tool? I noticed that this software works mainly with assembled sequences, since mine is not will i still be able to use this tool to predict functional profiles? Any advice will be much appreciated as trying to optimize my analysis pipeline.
Thank you in advance