Annotating and visualizing CLIP tags
chen chunxiao
Dear professor,
Hello! Thank you for a series of software developed by your research group, which gives users great convenience. I encountered some problems when using the iCLIP analysis method. I would like to consult you, and the problems are as follows:
Running bed2annotation. Pl script, I cant find the result of the error of the genome file/hg19 / annotation/hg19.genic.bed.Are these files has built good, still requires users to download by myself? Could you please share these files, or do you provide a download link?
Because hg38 was used for the previous analysis, I also tried hg38 here and prepared hg38.genic.bed by myself. However, there are still many files missing in the follow-up, so it seems that multiple built-in files are needed to complete this analysis.
It should be noted that since our environment is not compatible with peal, we have created a virtual environment as follows:
sudo docker start 3d2f47278420f88ecd5bb2e35d2cb5059db929d1eb74f024a221d2cb68ac1570
sudo docker exec -it brave_mclean bash
Since the beginning of mapping, I have run the sample code in the virtual environment. I wonder if it affected the error of the script in the virtual environment. If so, do you have any suggestions?
Or you can share files in:/ctk/annotation/genomes/hg38/annotation/ , maybe I can be added to the virtual environment for running.Thank you very much for your time and assistance.Looking forward to your reply!
best wish！
2024/03/04
Chunxiao Chen