Difference between revisions of "STAMP FAQs"
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| + | '''How can I fix my STAMP profile so it forms a strict hierarchy?''' | ||
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| + | A: The utility script [[Media:CheckHierarchy.zip|checkHierarchy.py]] can be used to identify entries within a STAMP profile that are not strictly hierarchical. These entries must be manually corrected. Often this is simply a matter of fixing up labeling errors or changing entries to indicate they are unclassified (e.g., changing ''uncultured bactrium'' to ''unclassified''). For taxonomic hierarchies, it may also be necessary to append the genus name to species names in order to make these unambiguous. In addition, the parent of all classified entries must also be classified. This can cause problems for some hierarchies such as GreenGenes and SILVA where sequences are assigned to specified OTUs, but intermediate taxonomic ranks are often unclassified. To handle this, I recommend removing the OTU column from the STAMP profile. If this level of precision is needed for certain analyses (e.g., PCA plots), a separate STAMP profile can be constructed which contains only the OTU column as the hierarchy. | ||
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| + | '''How can I fix my STAMP profile so all children have a classified parent?''' | ||
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| + | A: STAMP requires all children to have classified parents. Unfortunately, many existing taxonomies do not follow this practice. For example, the following in invalid in STAMP: ''Protebacteria->Gammaproteobacteria->unclassified->Enterobacteriaceae->Escherichia->E. coli'' as the order level designation is ''unclassified''. The easiest way to resolve this is to modify the taxonomy to take into account the last classified rank. Our example could be changed to: ''Protebacteria->Gammaproteobacteria->'''Gammaproteobacteria (order)'''->Enterobacteriaceae->Escherichia->E. coli''. | ||
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| + | Alternatively, you may choose to delete some columns from the STAMP profile if they are not required in your analysis and contain lots of unclassified entries (e.g., if the vast majority of Genus and Species level entries are unclassified and you only wish to do analyses at the order of family and above). | ||
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| + | '''How should I run my data through mothur for use with STAMP?''' | ||
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| + | STAMP is designed to work with the output from classify.seqs (http://www.mothur.org/wiki/Classify.seqs). Note, that you also need a group file (http://www.mothur.org/wiki/Group_file). | ||
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'''How do I request a new feature?''' | '''How do I request a new feature?''' | ||
| − | A: STAMP is in active development and we are interested in making it more useful for you. However, like yourself we have a limited amount of free time. If you have a feature suggestion please send an email to Rob Beiko (beiko [at] cs.dal.ca) with as much information as possible. We are open to collaborative efforts if major feature enhancements are being sought. Minor enhancements will generally be done on a first-come-first-serve-most-easily-done basis. If a minor enhancement is time sensitive (i.e., you are preparing a manuscript for publication) please indicate as much in your email. | + | A: STAMP is in active development and we are interested in making it more useful for you. However, like yourself, we have a limited amount of free time. If you have a feature suggestion, please send an email to Rob Beiko (beiko [at] cs.dal.ca) with as much information as possible. We are open to collaborative efforts if major feature enhancements are being sought. Minor enhancements will generally be done on a first-come-first-serve-most-easily-done basis. If a minor enhancement is time sensitive (i.e., you are preparing a manuscript for publication), please indicate as much in your email. |
'''How do I report a bug?''' | '''How do I report a bug?''' | ||
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'''Why does my Microsoft Windows installation of STAMP indicate the "configuration is incorrect"?''' | '''Why does my Microsoft Windows installation of STAMP indicate the "configuration is incorrect"?''' | ||
| − | If you have a pristine copy of Microsoft Windows installed you probably just need to install the Microsoft Visual C++ 2008 Redistributable Package ( | + | If you have a pristine copy of Microsoft Windows installed you probably just need to install the Microsoft Visual C++ 2008 Redistributable Package ([http://www.microsoft.com/downloads/details.aspx?FamilyID=9b2da534-3e03-4391-8a4d-074b9f2bc1bf&displaylang=en 32-bit], [http://www.microsoft.com/downloads/details.aspx?familyid=bd2a6171-e2d6-4230-b809-9a8d7548c1b6&displaylang=en 64-bit]). This package contains a number of commonly required runtime components. STAMP will fail with a message indicating the "configuration is incorrect" if you require this package. If this does not resolve your problem, please contact us. |
'''What license is STAMP released under?''' | '''What license is STAMP released under?''' | ||
STAMP is released under the [http://www.gnu.org/licenses/gpl.txt GNU General Public License]. | STAMP is released under the [http://www.gnu.org/licenses/gpl.txt GNU General Public License]. | ||
Latest revision as of 23:10, 3 November 2014
How can I fix my STAMP profile so it forms a strict hierarchy?
A: The utility script checkHierarchy.py can be used to identify entries within a STAMP profile that are not strictly hierarchical. These entries must be manually corrected. Often this is simply a matter of fixing up labeling errors or changing entries to indicate they are unclassified (e.g., changing uncultured bactrium to unclassified). For taxonomic hierarchies, it may also be necessary to append the genus name to species names in order to make these unambiguous. In addition, the parent of all classified entries must also be classified. This can cause problems for some hierarchies such as GreenGenes and SILVA where sequences are assigned to specified OTUs, but intermediate taxonomic ranks are often unclassified. To handle this, I recommend removing the OTU column from the STAMP profile. If this level of precision is needed for certain analyses (e.g., PCA plots), a separate STAMP profile can be constructed which contains only the OTU column as the hierarchy.
How can I fix my STAMP profile so all children have a classified parent?
A: STAMP requires all children to have classified parents. Unfortunately, many existing taxonomies do not follow this practice. For example, the following in invalid in STAMP: Protebacteria->Gammaproteobacteria->unclassified->Enterobacteriaceae->Escherichia->E. coli as the order level designation is unclassified. The easiest way to resolve this is to modify the taxonomy to take into account the last classified rank. Our example could be changed to: Protebacteria->Gammaproteobacteria->Gammaproteobacteria (order)->Enterobacteriaceae->Escherichia->E. coli.
Alternatively, you may choose to delete some columns from the STAMP profile if they are not required in your analysis and contain lots of unclassified entries (e.g., if the vast majority of Genus and Species level entries are unclassified and you only wish to do analyses at the order of family and above).
How should I run my data through mothur for use with STAMP?
STAMP is designed to work with the output from classify.seqs (http://www.mothur.org/wiki/Classify.seqs). Note, that you also need a group file (http://www.mothur.org/wiki/Group_file).
How do I request a new feature?
A: STAMP is in active development and we are interested in making it more useful for you. However, like yourself, we have a limited amount of free time. If you have a feature suggestion, please send an email to Rob Beiko (beiko [at] cs.dal.ca) with as much information as possible. We are open to collaborative efforts if major feature enhancements are being sought. Minor enhancements will generally be done on a first-come-first-serve-most-easily-done basis. If a minor enhancement is time sensitive (i.e., you are preparing a manuscript for publication), please indicate as much in your email.
How do I report a bug?
A: Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue.
How do I make my STAMP plugin available to the general public?
A: If you have created a plugin and would like to make it publicly available, we are happy to host it on this wiki. Plugins that will be of general use to STAMP users will be included in future releases (with your permission) and attributed to you. To have a plugin hosted on the STAMP website send an email to Rob Beiko (beiko [at] cs.dal.ca).
Why does my Microsoft Windows installation of STAMP indicate the "configuration is incorrect"?
If you have a pristine copy of Microsoft Windows installed you probably just need to install the Microsoft Visual C++ 2008 Redistributable Package (32-bit, 64-bit). This package contains a number of commonly required runtime components. STAMP will fail with a message indicating the "configuration is incorrect" if you require this package. If this does not resolve your problem, please contact us.
What license is STAMP released under?
STAMP is released under the GNU General Public License.
