text: user678: I have a set of RNA-seq samples from different experiments (Single and Paired End, depending on the experiment). I ran FASTQC in all the samples and found overrepresented adapter sequences:
  I removed the adaptors (TruSeq adaptors) using Cutadapt (in addition, I removed low quality and N bases from the 3' end of the reads). After that, I ran again FASTQC and the output is the following (representative example) :
  
  Does anyone know what is happening? Now I have an overrepresented sequence for which no sequence is provided. What does this mean? 
  
  user77: As @AaronBerlin mentioned, you didn't remove reads that were completely trimmed. Next time use the --minimum-length option and set it to something reasonable, like 20. Alternatively, use "Trim Galore!", which is a wrapper around cutadapt that has more reasonable defaults.
  
original_text: 678: <p>I have a set of RNA-seq samples from different experiments (Single and Paired End, depending on the experiment). I ran <a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" rel="noreferrer">FASTQC</a> in all the samples and found overrepresented adapter sequences:<a href="https://i.stack.imgur.com/RlZlZ.png" rel="noreferrer"><img src="https://i.stack.imgur.com/RlZlZ.png" alt="enter image description here"></a></p>
  
  <p>I removed the adaptors (TruSeq adaptors) using <a href="http://cutadapt.readthedocs.io/en/stable/guide.html" rel="noreferrer">Cutadapt</a> (in addition, I removed low quality and N bases from the 3' end of the reads). After that, I ran again FASTQC and the output is the following (representative example) :
  <a href="https://i.stack.imgur.com/tpgVR.png" rel="noreferrer"><img src="https://i.stack.imgur.com/tpgVR.png" alt="enter image description here"></a></p>
  
  <p>Does anyone know what is happening? Now I have an overrepresented sequence for which no sequence is provided. What does this mean? </p>
   77: <p>As @AaronBerlin mentioned, you didn't remove reads that were completely trimmed. Next time use the <code>--minimum-length</code> option and set it to something reasonable, like 20. Alternatively, use "Trim Galore!", which is a wrapper around cutadapt that has more reasonable defaults.</p>
  