<p>is it a good practice to remove all the <strong>unmapped</strong> reads with:</p>

<pre><code>samtools view -F 4
</code></pre>

<p>after they've been mapped with <strong>bwa</strong>  ? The <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> files would be smaller and the remaining operations would be faster isn't it ?</p>

<p>or shall I regret it later ?</p>

<p>To future-proof your data, it seems reasonable to hold on to the unmapped reads. For one, future algorithms may do a better job and allow you to recover some of that data. For another, future genome builds may resolve poorly assembled regions and allow additional reads to be mapped.</p>

<p>Neither of these improvements is likely to enable huge discoveries, but the cost you're paying in storage is pretty minimal, compared to the costs of sample collection and sequencing.  The speed hit probably isn't as bad as you think either, since the <a href='http://samtools.sourceforge.net/SAM1.pdf'>bam</a> is indexed. Smart algorithms will make use of that information and not even have to consider those unmapped reads.</p>
