how to get the fastq file from bax.h5 pacbio

[Fad2012]

Hello guys

Recently I have received my PacBio files from the company, which contain the sequencing results. The files are compressed (tar.bz2), when i extracted the file, I found only one file (name_of_the_file.bax.h5), I was wondering what would be the best way to analyse the file, as I am interested in the fastq file. How could i extract the fastq file?

Many thanks

[rhall]

What kind of analysis are you running on the data, you often need to run through some PacBio specific software before getting data that can be analysed using standard tools. Minimally PacBio's filtering pipeline should be used to generate fastq.
PacBio h5 format
Simple tool for manipulating PacBio h5 files

[Fad2012]

Thanks rhall

I am interested in the consensus subreads, fastq. I want to align against known reference for SNP detection

Many thanks

[rhall]

If you don't want to install the full SMRT Analysis system, I would at least use pbalign to align the data, which can use the bax.h5 files, then use quiver to call SNPs, you will get much better results than using other aligners of consensus callers.

[Fad2012]

Thanks very much Rhall, I will try this. Much appreciated.