chimeraslayer and pick_open_ref_otus.py

[Alana Shephard]

Hi,

I am using the pick_open_ref_otus.py with illumina V4 data, and am trying to incorporate chimera removal using ChimeraSlayer. I am slightly confused about how to feed the chimera-filtered pynast aligned sequences back into pick_open_ref_otus.py so it can continue with the filtering, building the phylogenetic tree and making the OTU table.

Is the correct way to proceed to run pick_open_ref_otus.py, filter chimeras from the pynast aligned seqs (identify_chimeric_seqs.py and filter_fasta.py), then perform each remaining step individually (filter_alignment.py, make_phylogeny.py and make_otu_table.py)? Or is there a way of feeding the chimera-filtered pynast aligned sequences back into pick_open_ref_otus.py?

I understand it is possible to chimera check prior to otu picking using usearch61, however I have read in this forum that qiime recommends chimera removal after otu picking? What do you recommend?

Sorry if I am misunderstanding and thanks for your help!

Alana.

[justink]

I think part of the confusion is that the program 'usearch61' does chimera filtering, as does chimeraslayer. If you're opting for chimeraslayer, the qiime devs typically recommend running identify_chimeric_seqs.py on the rep_set_aligned.fasta file.

I'm not sure about your bigger question of recommended chimeraslaying approaches. I will note that pick_open_reference_otus.py mitigates some of the chimera problems by comparing against a known database of sequences, such as greengenes.

[Rittik Deb]

Hi everyone,

I am also stuck in this same step. Is there a direct way to incorporate the chimeric_seqs.txt into the main pathway of open ref otu picking or we have to run many steps separately. Any answer will be very helpful.

Regards

Rittik

[justink]

Hi Rittik, sorry for the delay. I'm consulting a colleague and will let you know if I come up with anything useful.

[Rittik Deb]

Hi,

Please don't apologize and thanks a lot for you concern. Will be eagerly waiting for your reply.

Regards

Rittik