examples

Examples

In this example, we use the file circRNAs.gencode_format.tsv as the input.

1. Generating the references

To use the CircMiMi package, we need to generate the reference files first.

$ circmimi_tools genref --species hsa --source gencode --version 34 refs/

The above command will automatically download and generate the needed files from the "gencode release 34" and other databases.

2. Checking the circRNAs

$ circmimi_tools checking -r refs/ -i circRNAs.gencode_format.tsv -o circRNAs.gencode_format. --dist 5000

$ cat circRNAs.gencode_format.checking.results.tsv | awk -F'\t' '($9==1)&&($12==0)&&($16==1)' | cut -f '-5' > circRNAs.gencode_format.filtered.tsv

3. Predicting the interactions

$ circmimi_tools interactions -r refs/ -i circRNAs.gencode_format.filtered.tsv -o circRNAs.gencode_format. --miranda-sc 150

There are two output files:

• summary_list.tsv
• all_interactions.miRNA.tsv

For the format of these two files, please check the "Output files" section.

4. Visualization for the interactions

$ circmimi_tools visualize circRNAs.gencode_format.all_interactions.miRNA.tsv circRNAs.gencode_format.all_interactions.miRNA.xgmml