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Using MapMan

Mercator doesn't work for most of my FASTA

Hi,

I am working on Cannabis sativa RNA-seq. I want to get MapMan bins and then do enrichment analysis. I understand that since there isn't a mapping file for Cannabis at the Mercator store, I first have to generate it with Mercator. I upload my fasta file and it gave me an error, so I ran the fasta file validator. The error message that I get says that only 47 out of the 221 (!) sequences in the fasta file are valid. it says it is because of the length of these sequences. I obviously cannot run my analysis with a fasta that contains not even a quarter of all the sequences. I don't know what to do. This is the only reference fasta file available (downloaded directly from NCBI). How do I proceed? Please help