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Chimera.check

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Use chimeraCheck approach .... Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced.


Algorithm

Default settings

The fasta and template parameters are required. You may enter multiple fasta files by separating them by dashes. Example: fasta=ex.align-abrecovery.align.

mothur > chimera.check(fasta=ex.align, template=core_set_aligned.imputed.fasta)

The output to the screen looks like:

mothur > chimera.check(fasta=ex.align, template=core_set_aligned.imputed.fasta)
Reading query sequences... Done.
Reading in the core_set_aligned.imputed.fasta template sequences...	DONE.
Finding IS values for sequence 1
Finding IS values for sequence 2
...
Finding IS values for sequence 18


Opening ex.chimeracheck.chimeras you would see:

gi|11093941|MNA3|AF293013
IS scores: 	31	36	40	44	52	60	60	59	57	57 ...
gi|11093940|MNF8|AF293012
IS scores: 	35	43	46	49	55	57	58	62	71	71 ...
gi|11093939|MNB2|AF293011
IS scores: 	74	80	81	82	91	93	98	100     100	89 ...	
...

Options

ksize

The ksize parameter allows you to specify the size of the kmer to be used in determining the differences between sequence fragments. The default is 7.

mothur > chimera.check(fasta=ex.align, template=core_set_aligned.imputed.fasta, ksize=8)

svg

The svg parameter allows you to specify whether or not you would like a .svg file outputted for each query sequence. This can be helpful in visualizing the chimeric break. By default svg=false and no picture files are outputted.

mothur > chimera.check(fasta=ex.align, template=core_set_aligned.imputed.fasta, svg=t)

To see the .svg files for these sequences download svg files

name

The name parameter allows you to enter a file containing names of sequences you would like .svg files for. This can be helpful if you just want to look at the sequences that were determined to be chimeric by another method.

mothur > chimera.check(fasta=ex.align, template=core_set_aligned.imputed.fasta,
 name=potentialChimeras.names)

increment

The increment parameter is used to slide the window along the sequence. For the chimeracheck algorithm the default is 10.

mothur > chimera.check(fasta=ex.align, template=core_set_aligned.imputed.fasta, increment=50)

processors

To speed up your processing the chimera.check command can be run with multiple processors by using the processors parameter. By default the processors parameter is 1. If you are using the mpi-enabled version processors is set to the number of processes you have running.

mothur > chimera.check(fasta=ex.align, template=core_set_aligned.imputed.fasta, processors=2)

save

If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.