I am trying to use RSEM to receive relative abundance estimates of viruses within my metagenomic data, not transcripts. The problem is that I am no longer using Trinity as the assembler because I had much better luck with SPAdes, especially considering that I am not working with mRNA sequencing. Is it possible to use RSEM on a non Trinity assembly? If so, how do I go about doing so?
Note: I know that the SPAdes IDs provide a coverage meaurement for each individual contig; however, I need to compare the abundances of sequences across different samples and RSEM was good for that. What I mean is that I was able to pool all of my samples into one assembly, and RSEM would be able to differentiate the abundance of a certain sequence in each individual sample. If a sequence was assembled but only in one of my samples, RSEM would give me that information with the TPM measurements. If there is an alternative program I can use, please let me know!