Can RSII bax.h5 data be used?

[EdderDaniel]

Is there a way to use old RSII data (bax.h5 format) directly, or does it need to be transformed to bam?

[aseetharam]

@EdderDaniel, we have not tested it on RSII, but yes, it does need BAM file as input. If you want to try, please be sure to use subreads.

Thanks,

[EdderDaniel]

Thanks! I will try. do you have a suggestion on how to convert bax.h5 files into bam? I know that SMRT Link v7 has a function to do that but i cannot install it, so looking for alternatives for that :/

[aseetharam]

Sorry, I've not dealt with bax.h5 files for a while now, so not sure what works. However, a quick Google search brought this result up, which looks promising.
https://github.com/EichlerLab/bax2bam

Hope this helps!