to skip: extract reference reads

hi
can we skip this step of specifying position of our desired region, as i dont have primer sequence for my region of interest?
As I can understand that this is just to narrow down our search. correct me if m wrong
thanks

Hi @Nisha,

What function/command is this in reference to?

Best,
Justine

hi @jwdebelius

please see the following command

qiime feature-classifier extract-reads
–i-sequences 85_otus.qza
–p-f-primer GTGCCAGCMGCCGCGGTAA
–p-r-primer GGACTACHVGGGTWTCTAAT
–p-trunc-len 120
–p-min-length 100
–p-max-length 400
–o-reads ref-seqs.qza

Hi @Nisha,

Yes, you can skip this step. However, if you want to skip it, I would. recommend just getting a pre-trained classifier if you’re using a standard database.

Best,
Justine

hi @jwdebelius
so shall I use 99_otus.qza in place of ref-seqs.qza while trainning my classifier?

thanks
Nisha

Hi @Nisha,

I highly recommend downloading a pretrained classifier for your version of qiime2. There are already full length classifiers made for greengenes and silva. This way, you do the memory intensive process on someone else’s computer.

Otherwise, yes, you would use that as your rep-seq.qza.

Best,
Justine

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