Overrepresented kmers at the start of reads

[mattanswers]

Looking at the positions of the sequences, I would see if the sequences: CAGCACCAGCA or CAGCACCACC are part of your primers.

[pmiguel]

I agree. Probably reflects a sequence bias for the transposase used by Nextera. It will have its own agenda -- and it may not correspond perfectly with yours. But is it good enough? Assemble and see...

--
Phillip

[pbluescript]

I have seen Nextera libraries show a very similar bias. My guess is that this is just an artifact of the library prep. In the past, I would trim off these regions before mapping, but then I found that it didn't make a big difference, so I just left them there.

[kentk]

Is this RNA-Seq?

Its a bacterial genome run prepared using Nextera. And yes the %A, %T, %C, %G graph also looks like the kmer graph

[pbluescript]

Is this RNA-Seq? If so, this looks like it could be the result of random hexamer priming. Does the nucleotide distribution look off at the beginning too?

Hansen, K. D., S. E. Brenner, et al. (2010). "Biases in Illumina transcriptome sequencing caused by random hexamer priming." Nucleic Acids Research 38(12): e131.

[kentk]

I recently just discovered FastQC and I ran it in one of our datasets that's having difficulty in assembly. I was wondering how to interpret this piece of result from FastQC



Any ideas?