Can we use non base-called fast5 files in poretools? I run the MinION MinKNOW without the live base-calling option. We know there is Metrichor and Albacore to perform base-calling after this process. However, I have not done any base-calling yet.  

My question is: Is it possible to use directly the fast5 files with poretools to extract a fastq file without doing any previous base-calling process? I tried it and I get an empty fastq file. 

My reads directory only contains the fast5 folder and I run: 

poretools fastq fast5/ &gt; output.fastq

Any ideas why do I get an empty file? What is the difference between base-called fast5 and non-base-called fast5 files? 

Now I am trying to do base-calling with Albacore to see if I get a fastq file.
No, poretools does not do basecalling. The poretools fastq command can be used to extract the FASTQ information from the basecalled FAST5 file (via MinKNOW live-basecalling or albacore). Alternatively, both of these basecallers can export a FASTQ file directly if desired.

The difference between a basecalled FAST5 and a nonbasecalled FAST5 is the presence of the FASTQ within the file. This can be directly viewed using an HDF5 viewer, like h5dump from the commandline, or HDFView from the GUI.