Hi, Can the ITS1 and ITS2 for Fungi be done on the v3 chemistry 2x250bp Illumina?
Best wishes
Hi @Mantella86,
I'm no ITS expert so perhaps someone with more expertise can correct me if I'm off the target here. The challenge with ITS is that, unlike the rather uniform-length 16S region, ITS1 and ITS2 length can range substantially from very short to very long regions, depending on their lineage. How much of your community is made up of those shorter vs longer ranged ITS regions is highly dependent on your target samples, and so it is certainly an important consideration. Using 2x250 runs the risk of failing to merge certain "longer" clades and so may bias your results that way. That's not to say 2x300 will be perfect and bias-free either. My advise is to chat with someone who has lots of experience with the specific samples you are targeting (this forum included of course) and also dig into the literature to see the recommendation for those specific communities so at least you know your biases going on.
Hi @Mantella86,
To echo the points made by @Mehrbod_Estaki, I think this paper by Nguyen et al. 2015 provides a useful overview of things to consider about merging or not merging ITS data.
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