Length ratio between LTR and the internal region (-max_ratio) about ltr_retriever

[oushujun]

Hi Anand,

These are very careful thoughts. I believe we tried --max_ratio = 15KB / 100bp = 150 but it ended up too inclusive, which will result in very short LTRs flanking very long internal regions. Such a case is likely a nested insertion, either nested with LTR elements or other TEs, which will decrease the accuracy of the library. You may try it on your genome, and see if you find such extreme cases.

Other than the general length of LTR elements, we also noticed some extremely short or long elements during our curation. As short as 70bp for the LTR region, and as long as 20-30kb for the whole element, these elements are very difficult to discriminate between false positives based on the current algorithm, so we narrowed down the range for a more confident inference. 95% is just a rough estimate based on our library comparison with the manually curated library.

So far we don't see the necessity of controlling the internal length independently. We may implement it in the future if we find such a need. Please let me know if you have further questions.

Best,
Shujun