biais in GC content with illumina

[benR]

Hello everyone!

I am pretty new on this forum, and also in bacterial genome assembly. So you can expect I will have a lot of questions in the next few weeks (or months).

My first question is about a bias in the GC content in the first 10 bases of my reads. These reads are from a bacterial genome sequenced with Illumina. I read a lot about a bias like this in illumina, about a random priming not so random, but of course, it's for RNA seq, and I do not understand why it happens with genomic data...
I join a picture. I guess it's not a big deal, but i would like to understand.

Is anyone can help me to figured out what happen in my reads?
Thanks a lot

Ben

[AnotherHTS]

Was the library prepared with Nextera DNA Sample Prep? If so similar bias's have been reported

http://seqanswers.com/forums/archive/index.php/t-20561.html

[kcchan]

The Nextera bias is generally more severe than that. It generally has a very distinct pattern in the first 15 bases. This looks pretty standard for a sample sheared with sonication.

[benR]

Hi Another and kcchan,
Thank you very much for the replies !
I am not sure that the library was prepared with Nextera, i will asked. But i feel better to know this kind of bias is pretty standard in sequencing. SO you don't think I have to trim the first ten nucleotides.
Tahnks again
Ben

[MLog]

Hi benR,

just in case if you are still following this thread...
I don't know the reason, but I observe similar bias in most (if not all!) our DNA libraries (example attached). We are using Truseq library prep and fragmentation with Covaris. So this is probably not the Nextera problem.
Our bioinformaticians also had an idea that it would be better to trim these bases, but after we compared trimmed and non-trimmed data assembly we found that such trimming does not improve the results. So now we don't trim them.