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
Hi,

This is totally normal for RNA-sequencing data even after removal of the adapter sequences.
The random hexamer primers, which are used to generate the cDNA library from your RNA transcripts were shown to not bind completly random. This non-random binding leads to this bias in "per base sequence content" from base 1-15.

You don't have to trim these sequences, if fastqc does not report recognizes adapters. Just be aware, that the used primers do not lead to a completly random amplification.


