Oxford nanopore sequnces with unequal base content?

Question

[alexanderbeatovic450]

Hello everyone! First post here.

So we got hold of a new batch of nanopore sequences for a project we are working on. After base-calling I performed QC with fastqc. The per base sequence content module of the fastqc report worries me. Where one would expect a rather equal distribution of pairs of As and Ts, and Cs and Gs, our sequences have an unequal distribution. Is this a normal side effect of nanopore technology and can it be corrected with sufficient coverage or polishing with short reads? The per sequence base content report is attached below.

Looking forward to hearing your ideas on this.

All the best

[GenoMax]

Are these amplicons? Can you also try Nanoplot (LINK) to see what the data looks like?

[alexanderbeatovic450]

Not amplicons, genomic data

[GenoMax]

Since the intervals in plot are very large I would not worry too much about the plot yet. Try analyzing the data and see what happens.

[alexanderbeatovic450]

Thanks for the help!