chimera slayer finds always 0 chimeras when the SILVA123 database is used

[Massimiliano Cardinale]

Good day,
When I align my repset sequences with the greengenes database (core_set_aligned.fasta.imputed) and then run chimera slayer using the same core_set_aligned.fasta.imputed as reference and the pynast_aligned_repset as input, it detects several chimeras. But when I align THE SAME repset sequences with the new SILVA database (core_alignment_SILVA123.fasta fixed with fix_arb_fasta.py) and then run chimera slayer using the same fixed core_alignment_SILVA123.fasta as reference and the pynast_aligned_repset as input, it always finds no chimeras.
Please, can you explain me what I am doing wrong?

Thank you in advance,

Massimiliano

[Daniel McDonald]

Hi Massimiliano,

Different databases will yield different results, and chimera detection is rife with false positives and false negatives. I do recommend using UCHIME as the author of ChimeraSlayer recommends it over CS.

Best,

Daniel

[Massimiliano Cardinale]

Not the answer I expected... but thank you anyway. I am now trying to use Vsearch as standalone program on the seqs.fna file