Contigs with Ns

[ghost]

Hi PaPi,
Could you set a flag in the profiling to ignore contigs with Ns so they are not included in the analysis. Many assemblers will insert Ns for various reasons and it would be great to be able to control for this in the analysis.

[meren]

A contig with N's in one sample might be full of nucleotides in another. If you ignore the ones with N's in individual samples you can't do any merging / time series analyses. Apart from that, if a contig of 10,000 nucleotides has one N, should that be eliminated? If not, what should be the criterion?

I can add the option, but I want to make sure we are on the same page :)

[meren]

No followup. Maybe later.