I am a little bit confused about chimeric sequences removal in qiime1 and qiime2.
In qiime1 we remove chimeric sequences after assign taxonomy using identify_chimeric_seqs.py script whereas I can able to understand that in qiime2, dada2 remove chimeric by default.
Why there is two different approach?
Kind Regards
Yogesh
Hi @Yogesh_Gupta,
There is not really any reason to remove chimera after taxonomy assignment, it’s just a waste of computational resources to hold on to chimera that long — in qiime1 (to my knowledge) chimera removal was done either before or after OTU clustering.
Chimera removal happens at a similar time in QIIME 2: after OTU clustering or denoising. dada2 will remove chimera after denoising. If you use q2-vsearch for OTU clustering instead, you should use q2-vsearch for chimera removal.
See in qiime1
chimeric sequences were identified after alignment: using below command
identify_chimeric_seqs.py -m ChimeraSlayer -i seqs.fna_rep_set_aligned.fasta -a core_set_aligned.fasta.imputed -o seqs-chimeric_seqs_cs.txt
I need to ask you one more thing for OTU assignment I used below command is it correct to use -m rdp when providing fasta and taxonomy file
I first assign OTU using this command:
assign_taxonomy.py -i seqs.fna_rep_set.fasta –r 97_otus.fasta –t 97_otu_taxonomy.txt -m rdp
I used fasta and taxonomy file from latest greengenes database gg_13_8_otus.tar.gz
I am not sure -m rdp is correct to use here?
Okay, alignment and taxonomy classification are two entirely different things.
Your other questions are qiime1 questions — you will need to ask those on the qiime1 forum, I do not know the answer.
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