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Old 10-11-2015, 02:56 PM   #1
reubennowell
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Location: Edinburgh

Join Date: Jan 2013
Posts: 18
Default Import raw PacBio data from *.bax.h5 files

Dear all,

I've been sent some raw PacBio data from a collaborator which I'd like to import into SMRT Portal to generate filtered subreads and CCSs for scaffolding. However I'm struggling to understand the file structure for these data, in terms of what is needed for import into SMRT (and quite possibly PacBio data in general).

A description of the raw data: For each cell, I have three *.bax.h5 files, three *.subreads.fastq files and one *.metadata.xml. There is no *.bas.h5 file... I'm not sure why not. There is also a directory "error corrected" containing a corrected.fastq and a filtered_subreads.fastq.

I'm aware that SMRT requires a certain file structure (e.g., described in this link), and that the bas.h5 file is a pointer to the bax.h5 files. I'd like to know if it's possible to import these data into the SMRT software without the bas.h5, or if it's possible to generate a bas.h5 file from the files I do have?

I'm also a little unsure as to how the sequence files corrected.fastq and filtered_subreads.fastq have been generated - I am guessing that filtered_subreads.fastq contains the adapter-trimmed subreads (duh!), and that corrected.fastq contains the CCS sequences, but is there a way to know for certain?

Any insights will be greatly appreciated!
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