Example Use of Loop Annotaion and APA
This folder contains two subfolders that showcase example results of Polaris on loop prediction and aggregated peak analysis.
You can re-run Polaris to reproduce these results by following the commands provided in the sections below.
Note: If you encounter a
CUDA OUT OF MEMORYerror, please:
- Check your GPU's status and available memory.
- Reduce the --batchsize parameter. (The default value of 128 requires approximately 36GB of CUDA memory. Setting it to 24 will reduce the requirement to less than 10GB.)
Loop Prediction on GM12878 (250M Valid Read Pairs)
You can download example data from the Hugging Face repo of Polaris by runing:
wget https://huggingface.co/rr-ss/Polaris/resolve/main/example/loop_annotation/GM12878_250M.bcool?download=true -O "./loop_annotation/GM12878_250M.bcool"
And run following code to annotate loops from the example data:
polaris loop pred --chrom chr15,chr16,chr17 -i ./loop_annotation/GM12878_250M.bcool -o ./loop_annotation/GM12878_250M_chr151617_loops.bedpe
The loop_annotation sub-folder contains the results on bulk Hi-C data of GM12878 (250M valid read pairs).
APA of Loops Detected by Polaris
polaris util pileup --savefig ./APA/GM12878_250M_chr151617_loops.pileup.png --p2ll True ./loop_annotation/GM12878_250M_chr151617_loops.bedpe ./loop_annotation/GM12878_250M.bcool
The APA sub-folder contains the Aggregate Peak Analysis result of loops detected on GM12878 (250M Valid Read Pairs) by Polaris.
- Extensive documentation can be found at: Polaris Documentaion.
- You can find more detailed tutorials in the Jupyter Notebooks located within the respective subfolders.