Taxonomy for de-unique'd sequences

Commands in mothur
1

Is there any way to generate a taxonomy table for all sequences through Mothur, using the one generated by Classify.seqs?
Following the Mothur SOP, I generated taxonomy for the unique sequences, but I’m interested in having a table for all the quality reads, and I’d prefer not to reclassify 12 million reads if I can avoid it.

I am trying to see the effects of doing some 3’ pre-trimming on the paired .fastq files, and comparing it without any preprocessing using the vanilla MiSeq SOP. I am hoping to be able to generate .taxonomy for every redundant fasta sequence in both datasets, and parsing out the trimmed-vs-vanilla differences read-by-read.

Many Thanks!

2

Mothur does not have a way to create a complete *.taxonomy file from the unique taxonomy file and either a name or count file. You can run summary.tax to find the overall composition of the dataset.

mothur > summary.tax(taxonomy=yourUniqueTaxonomy, count=yourCountFile)

You can also merge tax summary files with the merge.taxsummary command, https://mothur.org/wiki/Merge.taxsummary.

3

Thanks!
I ended up grepping the names of the sequences in the .taxonomy file from the .names file (never thought all these intermediate files could be so useful :D)