Using VSEARCH for chimera and rep seq - reference based

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Sanjeev Sariya

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May 24, 2017, 4:05:35 PM5/24/17
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Hi QIIME Team,

Thanks for robust support and tool! I've been using VSEARCH with denovo clustering and chimera checking until now. However, I'm interested to use picrust, bugbase and these rely on greengenes database. 

I ran clustering using gg_13_8 database and seems bugbase needs ids as is from greengenes. 
I followed following procedure to get OTU table using VSEARCH and GG:

vsearch --derep_full full_tagclean.fasta  --output full_derep.fasta --log=vsearch_log --sizeout --minuniquesize 2 2>derep_log.txt
#dereplicate  seqs.fna 

vsearch -cluster_fast full_derep.fasta -id 0.97 --sizein --sizeout --relabel OTU_  --centroids otus.fna 2> cluster_log.txt
#cluster at 97%

vsearch --uchime_ref otus.fna --db 97_otus.fasta --nonchimeras otus_checked.fna --sizein --chimeras chimeras.fasta --borderline border_line.fasta --xsize 2> chimera_log.txt
#Pick OTUs at 97% threshold and use gg's 97% otu FASTA as reference db

vsearch -usearch_global full_tagclean.fasta -db otus_checked.fna -strand plus -id 0.97 -uc otu_table_mapping.uc --xsize 2> usearch_global_log.txt
#get .uc file

Later, process using robert edagr's python script to get OTU table.

1- Bugbase does't accept OTU ids with OTU_XXX and such. 
Is there a way I could retain database's IDs anywhere in these steps? I know this should be VSEARCH's question but don't know if this would be a appropriate query on their end. I'm using tools and guidance from QIIME developers and external collaborators so thought to ask here. Sorry. :(

2- Or, I use QIIME's scripts and have it do all of these themselves?

Looking forward to hear from you.

VSESARCH version: vsearch v2.0.3_osx_x86_64

Thanks,
Sanjeev

Colin Brislawn

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May 24, 2017, 5:17:53 PM5/24/17
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Hello Sanjeev,

This question may be a good fit for the picrust forms: https://groups.google.com/forum/#!forum/picrust-users 
You could also ask the vsearch devs, because they always looking for new ways to use vsearch and connect it with other bioinformatics software: https://groups.google.com/forum/#!forum/vsearch-forum

And finally, have you considered using vsearch to make a picrust compatible .biom table directly? Take a look at this tutorial for vsearch --> picrust.

I hope that helps,
Colin

Sanjeev Sariya

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May 25, 2017, 9:41:55 AM5/25/17
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Hi Colin,

Glad to hear from you. 

I get biom table as:
.uc file (from VSEARCH) --> make otu table from Robert edgar's scripts --> convert tab delimited otu table to biom using biom utility/commands

I've put my query on VSEARCH forum. 

Thanks,
Sanjeev


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