Hi, I need to relabel the sequence name for asv analysis. For otu, i can relabel it while i do get.oturep, but for asv, i have no idea. Could you give me how can i make relabel of my asv sequences like asv1, asv2…
This is important for me to generate the phylogenetic tree with similar name of shared file.
Sorry, but I’m not really sure what you’re asking. Have you seen how we generate ASVs in the MiSeq SOP? Each ASV has a unique sequence id (see the fasta file).
Thanks and sorry. Currently my fasta sequences have id like, >m64108e_220622_044535/98500950/ccs/rev
But i need to have it like >Asv00001
You could take the fasta and count files that represent your ASVs and run them through
rename.seqs. That will consecutively number the unique seqs from 1 to whatever.
Or, if Mothur could add the OTU number at the end of the taxonomy (as level 7) that would be sweet and kinda solve the problem? heheheh
The following command worked for me, get.oturep(list=samples.good.unique.good.filter.unique.precluster.denovo.vsearch.asv.list,fasta=samples.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta, count= samples.good.unique.good.filter.unique.precluster.denovo.vsearch.count_table, rename=T, method=abundance)