Answers.Body: <p>It worked, I installed a the newer version of deeptools, from GitHub:</p>
  <p><a href="https://github.com/deeptools/deepTools" rel="nofollow noreferrer">https://github.com/deeptools/deepTools</a></p>
  
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Answers.CreationDate: 2023-05-12T12:43:58.970Z
Answers.LastActivityDate: 2023-05-12T21:13:40.383Z
Answers.LastEditDate: 2023-05-12T21:13:40.383Z
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Body: <p>I am trying to get computeMatrix for bigwig file in specific genomic region using deeptools.<br />
  Below is the code I am using</p>
  <pre><code>computeMatrix reference-point --referencePoint TSS \
  -b 1000 -a 1000 \
  -R ~/Desktop/ATAC/ATAC/Inducible_elements_Greenberg.bed \
  -S ~/Desktop/ATAC/Control.mRp.clN.bigWig \
  --skipZeros \
  -o ~/Desktop/ATAC/matrix_controlmRPATACBasalcomputematrix.gz \
  </code></pre>
  <p>But I get the following error</p>
  <pre><code>File &quot;/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/__init__.py&quot;, line 305, in __getattr__
      raise AttributeError(__former_attrs__[attr])
  AttributeError: module 'numpy' has no attribute 'float'.
  `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
      https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'cfloat'?
  </code></pre>
  <p>These are the packages in my Conda environment</p>
  <pre><code># packages in environment at /Users/abhinavsoni/anaconda3/envs/ATAC_Seq:
  #
  # Name                    Version                   Build  Channel
  bzip2                     1.0.8                h3422bc3_4    conda-forge
  ca-certificates           2023.5.7             hf0a4a13_0    conda-forge
  libblas                   3.9.0           16_osxarm64_openblas    conda-forge
  libcblas                  3.9.0           16_osxarm64_openblas    conda-forge
  libcxx                    16.0.3               h4653b0c_0    conda-forge
  libffi                    3.4.2                h3422bc3_5    conda-forge
  libgfortran               5.0.0           12_2_0_hd922786_31    conda-forge
  libgfortran5              12.2.0              h0eea778_31    conda-forge
  liblapack                 3.9.0           16_osxarm64_openblas    conda-forge
  libopenblas               0.3.21          openmp_hc731615_3    conda-forge
  libsqlite                 3.41.2               hb31c410_1    conda-forge
  libzlib                   1.2.13               h03a7124_4    conda-forge
  llvm-openmp               16.0.3               h1c12783_0    conda-forge
  ncurses                   6.3                  h07bb92c_1    conda-forge
  numpy                     1.23.0          py310h0a343b5_0    conda-forge
  openssl                   3.1.0                h53f4e23_3    conda-forge
  pip                       23.1.2             pyhd8ed1ab_0    conda-forge
  python                    3.10.11         h3ba56d0_0_cpython    conda-forge
  python_abi                3.10                    3_cp310    conda-forge
  readline                  8.2                  h92ec313_1    conda-forge
  setuptools                67.7.2             pyhd8ed1ab_0    conda-forge
  tk                        8.6.12               he1e0b03_0    conda-forge
  tzdata                    2023c                h71feb2d_0    conda-forge
  wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
  xz                        5.2.6                h57fd34a_0    conda-forge
  </code></pre>
  <p>What could be its possible work around?</p>
  
Tags: <python><chip-seq><atac-seq><deeptools>
Title: Error while running computeMatrix command in Deeptools
ThreadText: # Error while running computeMatrix command in Deeptools
  
  (Asked by: username_0 on 2023-05-11)
  
  I am trying to get computeMatrix for bigwig file in specific genomic region using deeptools.  
  Below is the code I am using
  
  ```
  computeMatrix reference-point --referencePoint TSS \
  -b 1000 -a 1000 \
  -R ~/Desktop/ATAC/ATAC/Inducible_elements_Greenberg.bed \
  -S ~/Desktop/ATAC/Control.mRp.clN.bigWig \
  --skipZeros \
  -o ~/Desktop/ATAC/matrix_controlmRPATACBasalcomputematrix.gz \
  
  ```
  
  But I get the following error
  
  ```
  File "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/__init__.py", line 305, in __getattr__
      raise AttributeError(__former_attrs__[attr])
  AttributeError: module 'numpy' has no attribute 'float'.
  `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
  The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
      https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'cfloat'?
  
  ```
  
  These are the packages in my Conda environment
  
  ```
  # packages in environment at /Users/username_0/anaconda3/envs/ATAC_Seq:
  #
  # Name                    Version                   Build  Channel
  bzip2                     1.0.8                h3422bc3_4    conda-forge
  ca-certificates           2023.5.7             hf0a4a13_0    conda-forge
  libblas                   3.9.0           16_osxarm64_openblas    conda-forge
  libcblas                  3.9.0           16_osxarm64_openblas    conda-forge
  libcxx                    16.0.3               h4653b0c_0    conda-forge
  libffi                    3.4.2                h3422bc3_5    conda-forge
  libgfortran               5.0.0           12_2_0_hd922786_31    conda-forge
  libgfortran5              12.2.0              h0eea778_31    conda-forge
  liblapack                 3.9.0           16_osxarm64_openblas    conda-forge
  libopenblas               0.3.21          openmp_hc731615_3    conda-forge
  libsqlite                 3.41.2               hb31c410_1    conda-forge
  libzlib                   1.2.13               h03a7124_4    conda-forge
  llvm-openmp               16.0.3               h1c12783_0    conda-forge
  ncurses                   6.3                  h07bb92c_1    conda-forge
  numpy                     1.23.0          py310h0a343b5_0    conda-forge
  openssl                   3.1.0                h53f4e23_3    conda-forge
  pip                       23.1.2             pyhd8ed1ab_0    conda-forge
  python                    3.10.11         h3ba56d0_0_cpython    conda-forge
  python_abi                3.10                    3_cp310    conda-forge
  readline                  8.2                  h92ec313_1    conda-forge
  setuptools                67.7.2             pyhd8ed1ab_0    conda-forge
  tk                        8.6.12               he1e0b03_0    conda-forge
  tzdata                    2023c                h71feb2d_0    conda-forge
  wheel                     0.40.0             pyhd8ed1ab_0    conda-forge
  xz                        5.2.6                h57fd34a_0    conda-forge
  
  ```
  
  What could be its possible work around?
  
  **Tags:** python, chip-seq, atac-seq, deeptools
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-05-12. Score: 2
  
  It worked, I installed a the newer version of deeptools, from GitHub:
  
  <https://github.com/deeptools/deepTools>
  
  
  ---
  
  