Renaming the sequences in fasta file for asv based analysis

1

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.

2

Hi,

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).

pat

3

Thanks and sorry. Currently my fasta sequences have id like, >m64108e_220622_044535/98500950/ccs/rev

But i need to have it like >Asv00001

4

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.

Pat

5

Hello!

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? :slight_smile: heheheh

6

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)