Weihan Zhang

Hi Shujun, Thank you for your patience and help. I use CANU and set parameter minReadLength=20000, which set length >20kb were select as input for assembly. By CANU report I...

Hi Shujun, Thanks again for your patient help. ---------------------- Below is my LAI screen output: ``` ###################################### ### LTR Assembly Index (LAI) beta3.2 ### ###################################### Developer: Shujun Ou Please cite:...

Hi Shujun, I tried to polish the genome these days by Arrow and Pilon. However, Pilon is slower and still running, so I used NextPolish instead. For only Arrow polish,...

Hi Shujun, I just got the Pilon result and saw a significant improvement (LAI from 16.40 to 17.61) This is the LAI for Arrow (1 round) + Pilon (1 round)...

Hi Shujun, Thanks for your recent help. For the no polish genome LTR_retriever result (LAI = 16.38), the mean length of LTR regions is 6519.417. For the Arrow + Pilon...

Hi Shujun, Thanks for your correction, the following is my recalculation results. For the LAI = 16.38, the mean length of LTR regions is 5478.012. (no polish) For the LAI...

> hi,Shujun Ou, I get 2 different LAI value, value 1 was `whole_genome 1 272430828 0.0163 0.3975 4.09 6.80`, vaule 2 was `whole_genome 1 272430828 0.0161 0.1220 13.23 17.19`. >...

I also have the same problem. I have ~27K genes as universe genes, ~25k of them have GO annotation terms and as TERM2GENE, then I choose ~10k interesting genes to...

I have the same issue for augustus latest version clone from github. 'm going crazy, could anyone provide some help?

> Please provide minimal datasets for reproducing the problem. Weihan Zhang ***@***.***> schrieb am Di. 30. Apr. 2024 um 05:41: > […](#) > I have the same issue for augustus...