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Old 10-12-2015, 05:16 AM   #4
Location: Edinburgh

Join Date: Jan 2013
Posts: 18

Thanks for the replies both.

@GenoMax, yes I tried to import and received a "no SMRT cell data here" message from the Import SMRT Cells page. I agree this data appears to have been partly analysed; rather than trying to forensically determine what has been done I'd rather just reimport and reanalyse myself.

But I did get it imported in the end All that was required was to restructure the data like this:

|   |---*1.bax.h5
|   |---*2.bax.h5
|   |---*3.bax.h5
|   |---*1.bax.h5
|   |---*2.bax.h5
|   |---*3.bax.h5
|   etc.
|--- *.metadata.xml
|--- *.metadata.xml
In other words, mkdir Analysis_Results and then mv the bax.h5 files into there - the lack of a bas.h5 file didn't seem to be an issue.

As a side question, are there alternative programs apart from the SMRT software that allow you to go from a bax.h5 to filtered, trimmed and condensed (ie CCS) fastq?

Many thanks again.
reubennowell is offline   Reply With Quote