Description Usage Arguments Details Value Author(s) References See Also
Filter basecalling results to keep only high-quality bases
1 2 3 | ## S4 method for signature 'RolexaRun'
FilterResults(run=Rolexa.env,results)
FilterResults(run,...)
|
run |
a RolexaRun object defining the run parameters |
results |
a results object from |
... |
additional arguments, ignored |
FilterResults
filters the sequences according to the
entropy thresholds set by
IThresholds
and applies the
tag length cutoff
MinimumTagLength
.
The algorithm works as follows: for each tag the base entropies are
searched for a sub-vector k+1:l
such that
sum(entropy[n,5+k+1:l])<=IThresholds[l]
where l=MinimumTagLength
. If
such a sub-vector exists, it is then extended in both direction until the
total entropy exceeds the threshold:
sum(results[n,5+k1:k2])>IThresholds[k2-k1+1]
.
The tag is then shortened: substr(results[n,5],k1,k2)
, but [ACGT]
bases to left of k1
and to the right of k2
are
added. The Barcode
first bases of the tags
will always be included in a separate column if this parameter has
been set. If PET=TRUE
then the whole
procedure is applied independently to each half of the sequence (and
two separate sets of tags and scores are returned) and
the barcode (if any) is assumed to be in-between the two paired tags.
FilterResults
returns an object suitable for
SaveResults
Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef
Probabilistic base calling of Solexa sequencing data, BMC Bioinformatics 2008, 9:431
readFastq to read fastq files,
SeqScore
and FilterResults
to
produce results for SaveResults
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.