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| Removing Chimeras |
Removing
Chimeric Sequences From Your Report:
Greengenes uses Bellerophon to analyze
your aligned
sequences to eliminate any chimeric sequences that may have been
created during the PCR process. This is a multi-step process.
The first step is Greengenes reviewing the NAST summary file.
It reviews this file to see which sequences aligned
particularly
well. Sequences that aligned particularly well with a known
sequence within the Greengenes data base are not submitted to
Bellerophon for analysis. The assumption is that there are no
chimeric sequences in the Greengenes library and as such any sequence
aligning above a determined threshold with the library can also be
considered non-chimeric.
Only the remaining sequences are submitted to Bellerophon for
the
next steps in the chimeric check.
Step 1: Choosing
Which Files to Submit to Greengenes/Bellerophon
A) Use the "Browse" option to
search for the
FASTA file that you would like to have checked for chimeras.
B) Use the "Browse" option to
search for the
NAST summary that corresponds with the FASTA file you are submitting.
It is a document that ends with .xls. There is a
note to
make sure that your file is 'Tab Delimited'. As long as you
are
submitting the NAST summary returned to you by Greengenes with no
modifications or changes it is already 'Tab Delimited' and you need not
take any extra measures.
C) As is stated, this feature
is for the advanced user and you can disregard it here.
To proceed with the next step in doing a chimeric check, click here.
What
is a Chimera?
Greengenes
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