Hello,
I can not import my raw sequence in QIIME2 because I need to use FLASH to combine the pairs of read files with --allow-outie option after trimm and quality filter.
-O, --allow-outies Also try combining read pairs in the "outie"
orientation, e.g.
Read 1: <-----------
Read 2: ------------>
as opposed to only the "innie" orientation, e.g.
Read 1: <------------
Read 2: ----------->
FLASH uses the same parameters when trying each
orientation. If a read pair can be combined in
both "innie" and "outie" orientations, the
better-fitting one will be chosen using the same
scoring algorithm that FLASH normally uses.
Then, I can import my mergeALLreads.fasta into rep-seqs.qza with qiime tools import (type 'FeatureData[Sequence]').
But I don't know how is the next step, I mean, I have representative sequences (rep-seqs.qza) but I don't have the table.qza. Since qiime2 is working, OTUs has changed to ASVs, so, If I want to use dada2 or deblur for denoising, instead of OTU picking methods, I will need to start with the raw fastq, but if I can't do it?
Is there any procedure that the qiime2 starting point is joined-reads (rep-seqs.qza)?
Thanks for the help!