Identify_chimera.py using usearch61: Confused about the output

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Shebl E Salem

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Jan 6, 2016, 3:56:16 PM1/6/16
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Hi all,
I ran the following commands to identify and filter chimera sequences from my data

identify_chimeric_seqs.py -i Ion13And14And15Combined.fna -m usearch61 -o usearch_checked_chimeras131415/ -r 97_otus.fasta

 

filter_fasta.py -f Ion13And14And15Combined.fna -o 131415seqs_chimeras_filtered.fna -s usearch_checked_chimeras131415/chimeras.txt -n



I am not sure if the chimeras.txt output from usearch61 contains chimeras detected by both denovo and reference based detection or not?

Shebl E Salem

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Jan 7, 2016, 9:14:01 AM1/7/16
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Hi all,
I wonder if any one can help me with my previous questions (identify_chimeric_seqs.py using usearch61).
With my best wishes,
Shebl

TonyWalters

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Jan 7, 2016, 10:01:37 AM1/7/16
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Hello Shebl,

The chimeras.txt file does contain the sequences flagged as chimeras both by usearch's reference and de novo methods.

Shebl E Salem

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Jan 7, 2016, 10:10:08 AM1/7/16
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Hi Tony,
Thank you very much. I am so grateful to you.
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