chimera.perseus
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 when a sequence is found to be chimeric it is removed from it’s group, not the entire dataset.
Note: When you set dereplicate=t, mothur generates a new count table with the chimeras removed and counts adjusted by sample.
For a detailed example: Dereplicate example
removechimeras
The removechimeras parameter allow you to remove the chimeras from your files instead of just flagging them. Default=t.
Revisions
- 1.23.0 - First Introduced.
- 1.28.0 - added count parameter
- 1.29.0 - added dereplicate parameter
- 1.29.0 - Bug Fix: https://forum.mothur.org/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. - https://forum.mothur.org/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.
- 1.47.0 Adds removechimeras parameter to chimera commands to auto remove chimeras from files. #795
- 1.48.0 Significant speed improvements to command’s split by sample process.