text: user1421: 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/ > 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. 
  
  user681: Albacore can be used to create a fastq, directly from your fast5 files. As such there is no more reason to use poretools, expect perhaps for getting some metadata. With regards to metadata I would like to add that the sequencing_summary.txt generated by albacore also contains a lot of metadata.
  
  user92: 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.
  
original_text: 1421: <p>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.  </p>
  
  <p>My question is: Is it possible to use directly the <code>fast5</code> files with <code>poretools</code> to extract a fastq file without doing any previous base-calling process? I tried it and I get an empty fastq file. </p>
  
  <p>My <code>reads</code> directory only contains the <code>fast5</code> folder and I run: </p>
  
  <p><code>poretools fastq fast5/ &gt; output.fastq</code></p>
  
  <p>Any ideas why do I get an empty file? What is the difference between base-called <code>fast5</code> and non-base-called <code>fast5</code> files? </p>
  
  <p>Now I am trying to do base-calling with Albacore to see if I get a fastq file. </p>
   681: <p>Albacore can be used to create a fastq, directly from your fast5 files. As such there is no more reason to use poretools, expect perhaps for getting some metadata. With regards to metadata I would like to add that the sequencing_summary.txt generated by albacore also contains a lot of metadata.</p>
   92: <p>No, poretools does not do basecalling. The <code>poretools fastq</code> 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.</p>
  
  <p>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 <a href="https://support.hdfgroup.org/HDF5/doc/RM/Tools.html" rel="nofollow noreferrer">h5dump</a> from the commandline, or <a href="https://support.hdfgroup.org/products/java/hdfview/" rel="nofollow noreferrer">HDFView</a> from the GUI.</p>
  