How to filter chimera for post-deblur data?

[Listen-Lii]

Hi,
After running deblur, I got the reference-hit.seqs.fa like deblur / test / data / final.s4.seqs.fa.
How to filter chimera with this file?
By uchime_denovo command, it showed "Fatal error,cluster size not found".
By uchime3_denovo command, it showed "Missing input file name". The command is:
usearch10 -uchime3_denovo deblur/all_output/reference-hit.seqs.fa -uchimeout deblur/all_output/uchime/uchimeout.txt -chimeras deblur/all_output/uchime/chimera.fa -nonchimeras deblur/all_output/uchime/nonchimera.fa
Can anyone help me?

[amnona]

Hi, deblur does chimera removal as part of it's pipeline, so there should be no need to run chimera filtering after deblur. Deblur does the chimera removal after the denoising using vsearch --uchime_denovo. The parameter values used are: '-dn', '0.000001', '-xn', '1000', '-minh', '10000000', '--mindiffs', '5', The idea is to remove any sequence that is made up of 2 parts which are exact matches to other sequences. If you want to see the per sample deblurred fasta files before/after chimera removal, you can use the --keep-tmp-files flag (compare XXX.deblur and XXX.deblur.no_chimeras).

…

On Thu, Dec 28, 2017 at 9:21 AM, Listen-Lii ***@***.***> wrote: Hi, After running deblur, I got the reference-hit.seqs.fa like deblur / test / data / final.s4.seqs.fa. How to filter chimera with this file? By uchime_denovo command, it showed "Fatal error,cluster size not found". By uchime3_denovo command, it showed "Missing input file name". The command is: usearch10 -uchime3_denovo deblur/all_output/reference-hit.seqs.fa -uchimeout deblur/all_output/uchime/uchimeout.txt -chimeras deblur/all_output/uchime/chimera.fa -nonchimeras deblur/all_output/uchime/ nonchimera.fa Can anyone help me? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#165>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFkA8m0p3tSKOOuT3vHgLV01ifLZR0uRks5tE0F_gaJpZM4ROE19> .

[Listen-Lii]

Hi,
Amir et al. present that "after applying Deblur, only reads likely to have been presented to the sequencer are retained. However, it is possible that the reads would still contain chimeras originating from PCR"[1]. I misunderstood and thought chimera should be filtered by myself.
Thanks for your quick answer!

[1] Amir,A., D. McDonald, J. A. Navas-Molina, E. Kopylova, J. T. Morton, Z. Z. Xu, E. P.Kightley, L. R. Thompson, E. R. Hyde, A. Gonzalez and R. Knight (2017)."Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns."Msystems 2(2).

[wasade]

I believe this issue should be closed as there are no action items, please reopen if needed.