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Cooler Balance failed

1

Hi! I ran cooler balance with my cool file and it ran okay until it reached an error Output exceeds the size limit. Open the full output data in a...

kimquililan

Workaround TypeError exception raised by `cooler.annotate()` when bin ids in `/pixels` table are stored as unsigned integers. The exception is due to the implicit conversion to `float` performed by numpy...

robomics

How to create a one chromosome cool matrix

6

Hi, I am quite new with the cool format and I am not able to understand how to do this. I have a genome-wide .cool matrix and to perform some...

luciaalvarez95

iced matrix to cool

1

Hi author: When i run cooltools to identify the A/B compartment, I get an error message that 'Unable to open object (component not found)'. I guess this is input file...

Nuturetree

Restriction enzyme resolution crashes for fetch

1

Hi Nezar, I have created a cool matrix based on a restriction cut site resolution. If I try to load data via ``` cool_obj.matrix(sparse=True, as_pixels=False).fetch('chr1') ``` it is crashing. The...

joachimwolff

Installation on Windows 10

3

Hi, I am using Windows 10 and trying to install cooler package. When I try `pip install cooler` there seems a problem in installing 'pypairix' package and it is because...

ysora

cootools cis_eigs error

22

**Hello, I am using "cootools cis_eigs" for a multi-weighted .mcool file,** "cis_eigs=cooltools.eigs_cis(clr,gc_cov,view_df=view_df,n_eigs=3) eigenvector_track=cis_eigs[1][['chrom','start','end','E1']]" **but I've received the following error:** "ValueError Traceback (most recent call last) ~/opt/miniconda3/lib/python3.7/site-packages/cooltools/api/eigdecomp.py in eigs_cis(clr, phasing_track, view_df,...

hosseinsalari65

nvictus

I get the following warning from making .mcool files - ``` WARNING:py.warnings:/mmfs1/home/asur/.virtual/python-3/lib/python3.8/site-packages/cooler/util.py:733: FutureWarning: is_categorical is deprecated and will be removed in a future version. Use is_categorical_dtype instead is_cat = pd.api.types.is_categorical(bins["chrom"])...

aakashsur

Hello, after I use cooler dump to extract data, what exactly does count mean in the generated text file? like this：count chrom1 start1 end1 chrom2 start2 end2 count chr21 5030000...

tyewaichung