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Old 01-13-2017, 03:15 AM   #1
reubennowell
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Location: Edinburgh

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Default PacBio ENA SRA submission without bas.h5 files?

Dear all,

I've been sent some PacBio data from a collaborator that we now wish to submit to ENA. I've read that the way to do this is to create a manifest file, pointing to the 3 bax.h5 files, 1 bas.h5 file and 1 metadata.xml file for each cell (eg, this very useful post: http://seqanswers.com/forums/showthread.php?t=66767).

However, for some reason (I don't know why) the bas.h5 files are not present: within each cell dir there are 3 bax.h5 files, 3 subreads.fastq files and 1 metadata.xml file. As I did not generate these data myself I don't know their exact provenance I'm afraid - I don't know if the sequencing centre at which they were generated simply failed to ship these files to my collaborator, of if they were mislaid later.

The optimal solution would be to locate the missing files... but failing that, I wonder if anyone has had any experience of submitting to ENA without the bas.h5 files? Is it possible? Or, perhaps better, is there a tool/method that I can use to generate a bas.h5 file post hoc? My understanding of the bas.h5 files is that they are a "pointer" to the bax.h5 files, so maybe it's possible to make a new one.

Any tips or potential workarounds would be much appreciated!
Cheers!
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Old 01-13-2017, 05:42 AM   #2
GenoMax
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Those files should have been generated from the primary analysis of the PacBio run. See details here.

PacBio folks participate on the forum so perhaps they will have some advice later in the day.
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