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Difference between revisions of "Chimera.perseus"

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(Revisions)
 
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* 1.30.0 - Bug Fix: dereplicate=t, remove.seqs(dups=f) was not removing all redundant chimeras.
 
* 1.30.0 - Bug Fix: dereplicate=t, remove.seqs(dups=f) was not removing all redundant chimeras.
 
* 1.32.1 - Bug Fix: count table and dereplicate=t caused total=0 error message. - http://www.mothur.org/forum/viewtopic.php?f=4&t=2620
 
* 1.32.1 - Bug Fix: count table and dereplicate=t caused total=0 error message. - http://www.mothur.org/forum/viewtopic.php?f=4&t=2620
* 1.33.0 - improved work balance load between processors when processing by group.
+
* 1.33.0 - Improved work balance load between processors when processing by group.
* 1.40.0 Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.
+
* 1.40.0 - Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Latest revision as of 15:23, 29 March 2018

The chimera.perseus command reads a fasta and name file, and outputs potentially chimeric sequences.


Default Settings

The fasta and name or count parameters are required.

mothur > chimera.perseus(fasta=stool.trim.unique.good.filter.unique.precluster.fasta, name=stool.trim.unique.good.filter.unique.precluster.names)

or

mothur > chimera.perseus(fasta=stool.trim.unique.good.filter.unique.precluster.fasta, count=stool.trim.unique.good.filter.unique.precluster.count_table)


The output to the screen should look like:

Checking sequences from /Users/SarahsWork/Desktop/release/stool.trim.unique.good.filter.unique.precluster.fasta ...
Processing sequence: 100
Processing sequence: 200
Processing sequence: 300
Processing sequence: 400
...

Output in stool.trim.unique.good.filter.unique.precluster.perseus.chimeras:

SequenceIndex	Name	DiffsToBestMatch	BestMatchIndex	BestMatchName	DiffstToChimera	IndexofLeftParent	IndexOfRightParent	NameOfLeftParent	NameOfRightParent	DistanceToBestMatch	cIndex	(cIndex - singleDist)	loonIndex	MismatchesToChimera	MismatchToTrimera	ChimeraBreakPoint	LogisticProbability	TypeOfSequence
0	F21Fcsw_12128	0	0	Null	0	0	0	Null	Null	0.0	0.0	0.0	0	0	0	0.0	0.0	good
1	F11Fcsw_6529	0	0	Null	0	0	0	Null	Null	0.0	0.0	0.0	0	0	0	0.0	0.0	good
2	F11Fcsw_112161	0	0	Null	0	0	0	Null	Null	0.0	0.0	0.0	0	0	0	0.0	0.0	good
3	F21Fcsw_11639	40	0	F21Fcsw_12128	37	1	0	F11Fcsw_6529	F21Fcsw_12128	2.0468	1.93577	-0.111032	6.404	37	2147483647	55	0	good
4	F31Fcsw_127820	21	1	F11Fcsw_6529	20	1	0	F11Fcsw_6529	F21Fcsw_12128	1.07821	1.06372	-0.0144896	5.24698	20	2147483647	55	0	good
5	F11Fcsw_56988	12	1	F11Fcsw_6529	12	0	1	F21Fcsw_12128	F11Fcsw_6529	0.681584	0.681584	0	0.186912	12	2147483647	0	0	good
6	F21Fcsw_22694	39	1	F11Fcsw_6529	36	1	0	F11Fcsw_6529	F21Fcsw_12128	2.03523	1.91816	-0.117074	7.44773	36	2147483647	55	0	good
7	M11Fcsw_34015	25	1	F11Fcsw_6529	23	2	1	F11Fcsw_112161	F11Fcsw_6529	1.37518	1.26758	-0.107599	4.60899	23	21	15	0	good
8	F21Fcsw_85352	13	2	F11Fcsw_112161	12	1	2	F11Fcsw_6529	F11Fcsw_112161	0.739483	0.4676	-0.271884	14.2579	12	8	45	0	good
9	F11Fcsw_63768	53	2	F11Fcsw_112161	52	2	2	F11Fcsw_112161	F11Fcsw_112161	2.8013	2.79471	-0.00658628	0	52	50	28	0	good
10	F11Fcsw_46282	61	0	F21Fcsw_12128	58	0	2	F21Fcsw_12128	F11Fcsw_112161	3.33036	3.19547	-0.13489	8.87805	58	57	46	0	good
...

Options

group

If you provide a groupfile or a countfile that contains group information, mothur will process each sample individually and then combine the results.

mothur > chimera.perseus(fasta=stool.trim.unique.good.filter.unique.precluster.fasta, name=stool.trim.unique.good.filter.unique.precluster.names, group=stool.good.groups)

processsors

The processors parameter allows you to specify how many processors you would like to use. Default processors=Autodetect number of available processors and use all available.

alpha

The alpha parameter ... The default is -5.54.

beta

The beta parameter ... The default is 0.33.

cutoff

The cutoff parameter ... The default is 0.50.

dereplicate

The dereplicate parameter can be used when checking for chimeras by group. If the dereplicate parameter is false, then if one group finds the sequence to be chimeric, then all groups find it to be chimeric, default=f. If you set dereplicate=t, and then run remove.seqs with dups=f you can remove only the redundant chimeric sequences.

Let's look at an example:

>seq1
attgacat....
>seq4
ttgacaga....

seq1 seq1,seq2,seq3
seq4 seq4,seq5,seq6

seq1 group1
seq2 group2
seq3 group3
seq4 group1
seq5 group2
seq6 group3

If dereplicate=f and dups=t, (default settings in mothur), and seq2 is found to be chimeric by group2. The results would be:

>seq4
ttgacaga....

seq4 seq4,seq5,seq6

seq4 group1
seq5 group2
seq6 group3

If dereplicate=t and dups=t, and seq2 is found to be chimeric by group2. The results would be:

>seq4
ttgacaga....

seq4 seq4,seq5,seq6

seq4 group1
seq5 group2
seq6 group3

If dereplicate=t and dups=f, and seq2 is found to be chimeric by group2. The results would be:

>seq1
attgacat....
>seq4
ttgacaga....

seq1 seq1,seq3
seq4 seq4,seq5,seq6

seq1 group1
seq3 group3
seq4 group1
seq5 group2
seq6 group3


Revisions

  • 1.23.0 - First Introduced.
  • 1.28.0 - added count parameter
  • 1.29.0 - added dereplicate parameter
  • 1.29.0 - Bug Fix: http://www.mothur.org/forum/viewtopic.php?f=3&t=1656 - ignore N's
  • 1.30.0 - with count file and dereplicate=t will create a *.pick.count_table file.
  • 1.30.0 - Bug Fix: dereplicate=t, remove.seqs(dups=f) was not removing all redundant chimeras.
  • 1.32.1 - Bug Fix: count table and dereplicate=t caused total=0 error message. - http://www.mothur.org/forum/viewtopic.php?f=4&t=2620
  • 1.33.0 - Improved work balance load between processors when processing by group.
  • 1.40.0 - Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.