Hey guys:
I am doing **RNA-seq** analysis and it seems that the quality of my reads is not desirable.  
Below is **a typical fastqc report** for my data.  
I have read many tutorial about fastqc, from my understanding, **it seems that the 1-10 bp are adaptor sequences**.  But in the adaptor content section, there is no waining. 


----------


 - I am wandering if my understanding is right?
 - Should I use **trimmomatic** to cut adaptor sequences?  

![Failed per base sequence content][1]


  [1]: https://lh3.googleusercontent.com/Xp-_0jmKsw8p2MVrOx_X-hJbHIiKBfUFZ700lNT5nv0MKlma6DSgYonxLAbkHzkYNEaWHszNcvI6RjCPhk6YghTHfI7dT1_2GUyzPr4I5MdEnee1_qTSB46nbvwTJFh_TEASRgS1MEGIawbdc7zZpnWWd_bFL_CeNB0-MBk6PePyflSrMjeLZFlFu-1onTqcypuSMKeYw5Wty0c-pgPSCHWIHkTxrg3d0Y-XUhztxFRETL2sFQQXjtSGmZ5PhguduitzrZcnOijNlVK5KK_0hZ5Aqd-3pf7OHjJbRXfP02dxda5HQOrALIo-_DYoHszlbMDSFeLwSQerz80bPd2CNEsLmE79KsYBSqjOIeg_aH8npy70IlZc2pT34_pZul8pZapn_Yb_QN2tiazcaPPeYJvC-uVttpkoepsoaXT7Oz5lbB1OBkCrx1Ye3dyzpAx_bGhvdnnIXhOFYKbI44Nr1mh1ns7up0uj6uukZDqFOvRAkEFRNeNPHuqZlxGFfnCY1qAuM3Kqy3c0UjhVdDmFlTNVnR6wICnRR8v4EL7HxCbdPAnZ7JlHHzpaPHtKTxlMG80d51jSwWVLPa1GnaveRBsjfp3Ek5NVZ8bhv5UxhQXhPKRi8L3XBZ6-bg0t3MGomxWRSaE54EN6HD2GV1NKXE8muzTGcw=w1407-h809-no
The adapter starts at the 3' end of your reads, not the 5' (unless its an adapter dimer - i.e. no insert).

This is the result of random priming in RNA-Seq. I think [Biases in Illumina transcriptome sequencing caused by random hexamer priming][1] is the first paper on this. This represents real sequences. After alignment you can check the error rate in the reads, its only marginally higher 5' than in the rest of the read. And the fastqc report of the aligned sequences should show the same pattern.

  [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896536/