FastQC analysis on rrbs

Question

[Raphael]

Hi all,

I have checked my RRBS raw data (mouse DNA digested with MSPI and bisulfite converted) with fastQC and I have observed a decrease of the base sequence quality on position 2, it's occur in all of my 20 samples R1/R2, there is probably a link with the % of N content on position 2 also, but what can be the experimental reason of this decrease ? Has anyone obtain this kind of results with FastQC and have an idea ? Did there is something to do to improve the quality of my future rrbs ?

thanks a lot for your help

the link to the fastqc reports :

https://drive.google.com/file/d/1vIScAT6BW8TOAYLtoRZ5ihNFqMDsxX5v/view?usp=sharing https://drive.google.com/file/d/1NiBsoihfqp99kU3k6ZHtaDWunS88R0Iq/view?usp=sharing

Answer 1

[GenoMax]

Setting aside rrbs part this may simply be a problem with cycle 2 for this particular run e.g. a bubble went through the lane. Assuming the rest of the data looks ok (sorry not going to click on a random google drive link) you may simply want to hardtrim the first two-three bases. Alignment may also take care of soft-clipping these bad bases.

[Raphael]

Thank you GenoMax for your explanation. I will try the hardtrim