text: user3329: I tried to filter out FASTQ reads which are shorter than 259 bp with 
  bioawk -cfastx 'length() >= 259 {print "@" " " "\n""\n+\n"}' good/SZ005_NoIndex_L002_R1_009.good.fq.gz \
    | gzip >  good-filtered/SZ005_NoIndex_L002_R1_009.good-filtered.fq.gz`. 
  
  Unfortunately, the output was wrong:
  @ 
  
  +
  
  @ 
  
  +
  
  @ 
  
  What did I miss?
  Thank you in advance,
  
  user37: You need to use variable $seq. For example:
  bioawk -cfastx 'length($seq)>=259{print "@"$name"\n"$seq"\n+\n"$qual}' test.fq.gz
  
  There are also more convenient tools like seqtk and seqkit. With those, you may
  seqtk seq -L260 test.fq.gz
  
  
original_text: 3329: <p>I tried to filter out FASTQ reads which are shorter than 259 bp with </p>
  
  <pre><code>bioawk -cfastx 'length() &gt;= 259 {print "@" " " "\n""\n+\n"}' good/SZ005_NoIndex_L002_R1_009.good.fq.gz \
    | gzip &gt;  good-filtered/SZ005_NoIndex_L002_R1_009.good-filtered.fq.gz`. 
  </code></pre>
  
  <p>Unfortunately, the output was wrong:</p>
  
  <pre><code>@ 
  
  +
  
  @ 
  
  +
  
  @ 
  </code></pre>
  
  <p>What did I miss?</p>
  
  <p>Thank you in advance,</p>
   37: <p>You need to use variable <code>$seq</code>. For example:</p>
  
  <pre><code>bioawk -cfastx 'length($seq)&gt;=259{print "@"$name"\n"$seq"\n+\n"$qual}' test.fq.gz
  </code></pre>
  
  <p>There are also more convenient tools like <a href="https://github.com/lh3/seqtk" rel="nofollow noreferrer">seqtk</a> and <a href="https://github.com/shenwei356/seqkit" rel="nofollow noreferrer">seqkit</a>. With those, you may</p>
  
  <pre><code>seqtk seq -L260 test.fq.gz
  </code></pre>
  