Closed maharshi14 closed 2 years ago
Thank you for posting this. Based on the last two lines with the ValueError, it looks like the fetch method was expecting a chromosome name and got a filename name instead. Please inspect the cool file output by HiC-Pro and see what the chromosome labels are - this may be an oversight on my part with expecting chromosome labels to be compatible with specific string manipulations. If it's easy to rename chromosomes to something like ['1','2',...] or ['chrom1','chrom2',...] then try that next.
I hope this helps!
Hi, my suggestion is running "score_genome" instead of "score_chromosome" when you are using the pre-trained models for prediction. In your case, the command should be:
peakachu score_genome -r 10000 -p data.10kb.cool --balance -O output -m down1.h3k27ac.pkl
Keep in mind that although the model is named as "down1.h3k27ac.pkl", it was trained on GM12878 Hi-C data using H3K27ac HiChIP interactions as positive training set. You can have a try, but we cannot guarantee the prediction quality when you apply it to predict chromatin loops on HiChIP contact maps.
Xiaotao
Hi again,
The issue indeed was the chromosome annotations as 'chr1', 'chr2',...so on. Reprocessing my HiC-Pro output was indeed the trick. Thank you!
Hello,
Thank you for creating this tool.
I'm attempting to run Peakachu on my H3K27ac HiChIP data with total number of intra-chromosomal pairs = 65634708. I've downloaded the H3K27ac 1.5% model file for this, the size of which is ~4.4M and is called down1.h3k27ac.pkl.
My .cool file is of resolution 10kb, which I created from a .hic file (using HiC-Pro), converted using
hic2cool
and then normalised usingcooler balance
.After running
peakachu score_chromosome -r 10000 --balance -p data.10kb.cool -O output -m down1.h3k27ac.pkl
, I keep getting the following error messages pertaining to the model file:Any troubleshooting on this would be greatly appreciated. Thank you!