<p>I am getting the following error with fastx_quality_stats with version 0.0.13.2. May be this has to do with the changing Illumina scores. Now they are Phred33 I believe. Has anyone seen this issue</p>

<pre><code>fastx_quality_stats -i test.fastq 
fastx_quality_stats: Invalid quality score value (char ')' ord 41 quality value -23) on line 4
</code></pre>

<p>Thanks!
-Abhi</p>

<pre><code>more test.fastq 
@HISEQ08:235:D142MACXX:7:1101:1474:2097 1:N:0:CGATGT
CCCTCTCCTTCTCCCAGGTAGAACGAGCCTCCCTTTCCCTAGTCAGGGAGTCTTCAAGGAGTTTCTCCTTTGCTGCTGACTTGTCTTTGAATTGCTTGTGGCGTTTTGGAACTTCCTCTTCATTAAGAATCTAGGGTTGTG
CAATTTTCT
+
??&lt;DDD=:C&gt;:CC@A@EEE@C:4:F)@?EDDDD3?B??B9?B?9BD3@@@BC&gt;@CEIIEA=C@?=??. ########################################################################
#########
</code></pre>

<p>A quick google returns: <a href='http://seqanswers.com/forums/archive/index.php/t-7596.html'>http://seqanswers.com/forums/archive/index.php/t-7596.html</a></p>

<blockquote>
  <p>ou need to add the -Q33 parameter to tell it that you're using
  Illumina encoded quality scores, not Sanger encoding.</p>
</blockquote>
