search

weir12 / DENA

Deep learning model used to detect RNA m6a with read level based on the Nanopore direct RNA data.
MIT License
22 stars 5 forks source link

about m6A validation set #13

Closed xieyy46 closed 2 years ago

xieyy46 commented 2 years ago

Hi DENA team! I' d want to know how you get the 4685 miCLIP sites identified in Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification, while I found that the number of miCLIP sites identified in Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification was 93046. image

weir12 commented 2 years ago

Hi, I am sorry for the late reply due to the covid-19 pandemic. The miCLIP data for both the original sites (93046) and the filtered sites (4685) were obtained by email contact with the corresponding author of Gao Y, Liu X, Wu B, Wang H, Xi F, Kohnen MV, Reddy ASN, Gu L. Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing. Genome Biol. 2021 Jan 7;22(1):22. doi: 10.1186/s13059-020-02241-7. PMID: 33413586; PMCID: PMC7791831.

If you would like to get the original miclip data or the data processing strategy, please contact the author Gu L or Gao Y.

This is the email we used to use (availability unconfirmed now). lfgu@fafu.edu.cn