Hello Simon,
You are correct, Galaxy does not have a tool to do this exact operation
in one step, but the "Join, Subtract and Group -> Group" tool may be
able to generate the statistics you want from a tabular file containing
the linked data. Such as: clusterID -> sequenceID -> barcodeID. Creating
this file would require an uploaded clusterID -> sequenceID file and
extracted sequenceID -> barcodeID data resulting from the "NGS: QC and
manipulation -> Barcode splitter" tool. These two could be joined with
"Join, Subtract and Group -> Join two Datasets" on the common identifier
sequenceID. The processing would be multi-stepped, but once developed,
the Galaxy steps could be saved in a workflow to run in the future.
Best wishes for your research project,
Jen
Galaxy team
On 11/23/11 2:30 AM, Simon Bulman wrote:
Dear Galaxy
we have a 454 metagenomic dataset. We have used barcode splitter to
divide the dataset into it's constituent amplicons. We have also been
using a clustering application (dnaclust) in Galaxy to subdivide the
dataset by similarity. My question is; are there Galaxy tools to allow
the combining, sorting and counting of these two outputs? For example,
can each cluster - and then each sequence within that cluster - be given
an identifier.... so that one can then split the output by barcode and
summarise the data along the lines of amplicon/barcode X has X number of
sequences within cluster 1, X number of sequences within cluster 2, ...
etc? Am I making any sense?
This is the sort of problem that sounds like it is solvable in Excel
and, indeed, a UK colleague of mine has been doing just this. But is
there a straightforward means to do so in Galaxy? It is not obvious to
me in the Filtering or Sorting tools.
best wishes
Simon
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