I have some rna-seq data and they all have this odd extra peak in GC content. Adapter trimming was carried out using Skewer to produce trimmed reads. The adapter contamination is now gone but the GC profile still looks strange. Is this something I need to be concerned about? Is there a way to pull out or examine the reads that constitute this extra peak? I also noticed that the kmer profile has changed after trimming especially in the 3' end.

![fastqc plots][1]

  [1]: http://s32.postimg.org/ec1w140g5/fastqc_small.jpg
In your final plots we can see that there is a sequence of DNA common to a very large proportion of your reads that occurs at the start and/or end of your reads. Trying to glue those kmers together in my head I think you end up with 2 distinct adapter sequences: "GCCGGCATCACCGCG", and "GTCGGCATCACCGCG" which are obviously both highly GC rich, but one is 2% higher than the other.

I believe this would be the cause of your other peak(s), and if you can find a way to trim that stuff off your reads, you'll be fine.
You can test this if you like with [SeQC][1], but you'd need to have a .stat method for identifying reads as starting with GCCGGCATCACCGCG. I could make one for you very quickly if you don't know python.


  [1]: https://github.com/JohnLonginotto/SeQC