Hi everyone !
I'm new to PacBio long reads sequencing and I've read a lot about what exactly contains the raws files produced by this type of sequencer. I understand that the two different tpyes (.bas.h5 and .bax.h5) refer to what each file contains (sequence, quality value, information about the chemistry used...).
But as a beginner, I still don't understand how to transform theses .bax.h5 files into a subreads.fastq files, and also I don't know what exactly to give to a assembly pipeline (I'm using Falcon), should I give a fastq file or a .bax.h5 file ?
I've got the same problem for the polishing step with Quiver that require the quality informations contained in original files.
I really need some explanations about that, if you could please give me some advices !