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Difference between revisions of "Chimera.ccode"

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Line 197: Line 197:
  
 
  mothur > chimera.ccode(fasta=ex.align, template=core_set_aligned.imputed.fasta, processors=2)
 
  mothur > chimera.ccode(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.
 
  
 
This method was written using the algorithms described in the "Evaluating putative chimeric sequences from PCR-amplified products" paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.
 
This method was written using the algorithms described in the "Evaluating putative chimeric sequences from PCR-amplified products" paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.
 +
 +
==Revisions==
 +
* 1.38.0 - Removes save option.
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Latest revision as of 17:01, 20 July 2016

Use Ccode approach ....


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.ccode(fasta=ex.align, template=core_set_aligned.imputed.fasta)

The output to the screen looks like:

mothur > chimera.ccode(fasta=ex.align, template=core_set_aligned.imputed.fasta)
Reading sequences and template file... Done.
Finding top matches for sequences... Done.

gi|11093940|MNF8|AF293012 was found have at least one chimeric window.
gi|11093937|MNF2|AF293009 was found have at least one chimeric window.
gi|11093934|MND1|AF293006 was found have at least one chimeric window.
gi|11093933|MNA5|AF293005 was found have at least one chimeric window.
gi|11093932|MNA1|AF293004 was found have at least one chimeric window.
gi|11093930|MNH4|AF293002 was found have at least one chimeric window.
gi|11093926|MNH2|AF292998 was found have at least one chimeric window.
gi|11093924|MNF4|AF292996 was found have at least one chimeric window.

Opening ex.ccode.chimeras you would see:

For full window mapping info refer to ex.mapinfo
...
gi|11093940|MNF8|AF293012

Reference sequences used and distance to query:
1456	0.124
141312	0.138
102418	0.140
110103	0.149
183441	0.234
99346	0.236
142598	0.239
136664	0.239
1443	0.251
216057	0.256
70898	0.262
167370	0.263
10709	0.264
225365	0.265
168547	0.265
27824	0.268
10686	0.269
10763	0.269
147978	0.269
123055	0.269


Mapping information: 
Window	StartPos	EndPos
1	108	778
2	778	1448
3	1448	2118
4	2118	2788
5	2788	3458
6	3458	4128
7	4128	4798
8	4798	5468
9	5468	6138
10	6138	6808
11	6808	6812

Window	AvgQ	(sdQ)	AvgR	(sdR)	Ratio	Anova
1	47.550	20.109	54.095	11.853	0.879	4.709
2	21.350	8.677	21.711	5.681	0.983	0.065
3	43.250	20.749	49.658	13.050	0.871	3.829
4	49.050	16.863	50.247	11.667	0.976	0.173
5	0.001	0.001	0.001	0.001	1.000	0.004
6	16.350	8.916	20.821	7.403	0.785	6.340
7	45.150	10.811	46.626	12.730	0.968	0.250
8	29.600	5.020	25.779	7.435	1.148	5.029
9	30.650	3.345	24.074	7.534	1.273	14.877
10	54.500	6.126	44.747	13.275	1.218	10.523
11	0.450	0.510	0.521	0.501	0.864	0.363

Window	ConfidenceLimit	t-Student	Anova
1				
2				
3				
4				
5				
6				
7				
8		*	*	
9	*	*	*	
10		*	*	
11				

...

The * indicate that the window was found to be chimeric using the given limits.

Options

filter

By default the filter parameter is set to false, but if you set it to true a 50% soft vertical filter will be applied.

mothur > chimera.ccode(fasta=ex.align, template=core_set_aligned.imputed.fasta, filter=t)
Reading sequences and template file... Done.
Finding top matches for sequences... Done.
Filter removed 6397 columns.

gi|11093940|MNF8|AF293012 was found have at least one chimeric window.
gi|11093939|MNB2|AF293011 was found have at least one chimeric window.
gi|11093937|MNF2|AF293009 was found have at least one chimeric window.
gi|11093934|MND1|AF293006 was found have at least one chimeric window.
gi|11093932|MNA1|AF293004 was found have at least one chimeric window.
gi|11093930|MNH4|AF293002 was found have at least one chimeric window.
gi|11093926|MNH2|AF292998 was found have at least one chimeric window.
gi|11093924|MNF4|AF292996 was found have at least one chimeric window.


mask

By default there is no mask applied, but you can set it to a file containing your mask or mask=default will apply the ecoli mask.

mothur > chimera.ccode(fasta=ex.align, template=core_set_aligned.imputed.fasta, mask=default)
I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013.
Reading sequences and template file... Done.
Finding top matches for sequences... Done.
gi|11093939|MNB2|AF293011 does not have an adaquate number of reference sequences that are within 20% and 0.5%
similarity.  I will continue, but please check.
gi|11093941|MNA3|AF293013 was found have at least one chimeric window.
gi|11093940|MNF8|AF293012 was found have at least one chimeric window.
gi|11093939|MNB2|AF293011 was found have at least one chimeric window.
gi|11093938|MNC2|AF293010 was found have at least one chimeric window.
gi|11093937|MNF2|AF293009 was found have at least one chimeric window.
gi|11093934|MND1|AF293006 was found have at least one chimeric window.
gi|11093933|MNA5|AF293005 was found have at least one chimeric window.
gi|11093930|MNH4|AF293002 was found have at least one chimeric window.
gi|11093926|MNH2|AF292998 was found have at least one chimeric window.
gi|11093924|MNF4|AF292996 was found have at least one chimeric window.


With the ecoli mask and filter applied...

mothur > chimera.ccode(fasta=ex.align, template=core_set_aligned.imputed.fasta, mask=default, filter=t)
I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013.
Reading sequences and template file... Done.
Finding top matches for sequences... Done.
Filter removed 259 columns.

gi|11093940|MNF8|AF293012 was found have at least one chimeric window.
gi|11093939|MNB2|AF293011 was found have at least one chimeric window.
gi|11093937|MNF2|AF293009 was found have at least one chimeric window.
gi|11093934|MND1|AF293006 was found have at least one chimeric window.
gi|11093932|MNA1|AF293004 was found have at least one chimeric window.
gi|11093930|MNH4|AF293002 was found have at least one chimeric window.
gi|11093926|MNH2|AF292998 was found have at least one chimeric window.

window

The window parameter is used to determine the length of sequence you want in each window analyzed. By default it is set to 10% of the sequence length. It is recommended that your window size be within 5 and 20% of your trimmed sequence length.

mothur > chimera.ccode(fasta=ex.align, template=core_set_aligned.imputed.fasta, window=400)
Reading sequences and template file... Done.
Finding top matches for sequences... Done.

gi|11093940|MNF8|AF293012 was found have at least one chimeric window.
gi|11093939|MNB2|AF293011 was found have at least one chimeric window.
gi|11093937|MNF2|AF293009 was found have at least one chimeric window.
gi|11093934|MND1|AF293006 was found have at least one chimeric window.
gi|11093932|MNA1|AF293004 was found have at least one chimeric window.
gi|11093930|MNH4|AF293002 was found have at least one chimeric window.
gi|11093929|MNC12|AF293001 was found have at least one chimeric window.
gi|11093928|MNG3|AF293000 was found have at least one chimeric window.
gi|11093926|MNH2|AF292998 was found have at least one chimeric window.


numwanted

The numwanted parameter allows you to specify how many sequences you would each query sequence compared with. By default it is set to 20.

mothur > chimera.ccode(fasta=ex.align, template=core_set_aligned.imputed.fasta, numwanted=10)
Reading sequences and template file... Done.
Finding top matches for sequences... Done.
gi|11093940|MNF8|AF293012 was found have at least one chimeric window.
gi|11093937|MNF2|AF293009 was found have at least one chimeric window.
gi|11093934|MND1|AF293006 was found have at least one chimeric window.
gi|11093933|MNA5|AF293005 was found have at least one chimeric window.
gi|11093932|MNA1|AF293004 was found have at least one chimeric window.
gi|11093930|MNH4|AF293002 was found have at least one chimeric window.
gi|11093926|MNH2|AF292998 was found have at least one chimeric window.


processors

To speed up your processing the chimera.ccode 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 running.

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

This method was written using the algorithms described in the "Evaluating putative chimeric sequences from PCR-amplified products" paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.

Revisions

  • 1.38.0 - Removes save option.