Has any one created a MetaSIM error profile file (.mconf) for Illumina reads >100bp?

Question

[Tawny]

I am considering using MetaSIM to create a metagenomic synthetic reads dataset. I want to use an Illumina error profile. I see that MetaSIM includes Illumina error profile files for 36bp and 80bp read lengths. In their manual they say you can create your own error profile, the .mocnf file. I need an error profile for reads that are longer than 100bp.

Does anyone have experience with creating an error profile file for MetaSIM that covers longer reads?

[beacamara]

Hello Tawny!

I have no the same problem as you had several months ago. I would like to create a MetaSim empirical error model file (.mconf) for Ilumina reads 100 bp. Did you solve this problem? What did you do?

Thank you so much

Beatriz

[Tawny]

I ended up using the error profile that is provided with MetaSIM and just expanding it. So I added new rows with similar values until I reached the read length I needed for my project. Then I plotted my revised profile file so I could look at it and make sure it looked like what I would expect for an Illumina run of the same read length. My plot had a few unusual dips so I went back and tweaked the values I added to the error model until I got a plot that reflected what I have seen in real data.

[beacamara]

Thank you so much Tawny. I see what you mean. I was thinking in doing something similar but I was not sure if it was right. In the FAQ section of MetaSim there is a light explanation on this aspect, but not enough to understand it.

Thank you so much

Bea