Kamil Slowikowski

Hi Zhen, Thanks for opening an issue! If you could share a minimal example of code and subset of your data that reproduces this error, I can try to run...

Please feel free to reopen this issue if you can provide a minimal example.

Hi Vatsal, thanks for sharing your code and error. That helps. If your session is still live, it would help if you run `traceback()` so we can see which line...

Hi Hu, you might consider reading the other related issues: - #9 - #2

Yes, gzip will throw that error when you try to decompress (`gunzip`) a file that is not compressed. You only need to decompress a file when it is compressed (it...

I think you caught a typo in my tutorial! Thanks for reporting it. I haven't tested it, but I think the correct command is: ``` cat chr*.fa.masked > hg19.fa ```...

It looks like the particular files I used in the tutorial have been archived. You should find a different study that interests you: https://www.encodeproject.org/search/?type=Experiment&assay_term_name=DNase-seq&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens Here is [one possible example][1], showing...

Thanks for the question! At the time of writing, I was mostly concerned with how to get the data into the right format so that we can run CENTIPEDE in...

After reading the supplement again, I think you're right. Thanks for pointing out the difference. It seems the authors consider all sites that have an approximate PWM match, regardless of...

Thanks for reporting this issue! This is a duplicate of #32. I think we can fix the issue, but it is low priority right now.