I am doing circDNA prediction, as there is not softwere yet available. So I want to generate pipeline for it. Can anybody tell me how to setup pipeline for this type of data. I have tried CIRI but it detected circRNA, not circDNA. I need circDNA.
Dear Abdul,
We have publish today on biorvix a preprint with a new algorithm for circular DNA detection.
https://www.biorxiv.org/content/10.1101/654194v1
The code is now publicly available via github (https://github.com/iprada/Circle-Map) and it contains a step-by-step tutorial (https://github.com/iprada/Circle-Map/wiki/Tutorial:-Identification-of-circular-DNA-using-Circle-Map-Realign) explaining how to go from the raw data to interpretable results.
I hope it helps!
Dear Abdul,
Thanks for using Circle-Map.
The reason you are getting the error is because your system is using bash and not python to interpret the code. And of course, bash does not understand python. I think that this error was caused because the source code was directly downloaded from github instead of using the installations recipes.
I recommend this two solutions:
I did create easy installation recipes for pip and conda, so that the software and its dependencies where easy to install. You can install the software using pip with the following command ( needs python >=3):
python -m pip install Circle-Map
And with conda using a similar flavour:
conda install -c bioconda circle-map
This should solve your issue. Let me know if this helps,
Best wishes
Iñigo
Thanks for your quick response, The commands you have mentioned above are still not working with me.
[skabdul@mn02 M1]$ python -m pip install Circle-Map
/bin/python: No module named pip
[skabdul@mn02 M1]$ conda install -c bioconda circle-map
Fetching package metadata ...........
Solving package specifications:
PackageNotFoundError: Packages missing in current channels:
- circle-map -> biopython >=1.73
- circle-map -> numba >=0.43.1
- circle-map -> numpy >=1.16.3
- circle-map -> pandas >=0.24.2
- circle-map -> pybedtools >=0.8.0 -> libgcc-ng >=4.9
- circle-map -> pybedtools >=0.8.0 -> libstdcxx-ng >=7.3.0
- circle-map -> scipy >=1.2.1
- circle-map -> tqdm >=4.31.1
We have searched for the packages in the following channels:
- https://conda.anaconda.org/bioconda/linux-64
- https://conda.anaconda.org/bioconda/noarch
- https://repo.continuum.io/pkgs/free/linux-64
- https://repo.continuum.io/pkgs/free/noarch
- https://repo.continuum.io/pkgs/r/linux-64
- https://repo.continuum.io/pkgs/r/noarch
- https://repo.continuum.io/pkgs/pro/linux-64
- https://repo.continuum.io/pkgs/pro/noarch
Dear Abdul,
Regarding the error with the python installation, probably you have a python version lower than 3.0. Circle-Map is implemented on python 3.6 and I do not plan to support versions of python lower than that. I have update the github readme accordingly. Sorry for the confusion. What is the output of:
python --version
Regarding the error with the conda installation, the conda installer is not able to find packages outside the bioconda channel. Try running the following commands:
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
And then try to install Circle-Map as before:
conda install -c bioconda circle-map
This should allow conda to find the missing Circle-Map dependencies. Let me know if this helps
Best wishes,
Iñigo
Same error has showing, even I have Python 3.6 and installed the conda dependencies.
[skabdul@mn02 M1]$ python --version
Python 3.6.5
[skabdul@mn02 M1]$ conda config --add channels defaults
Warning: 'defaults' already in 'channels' list, moving to the top
[skabdul@mn02 M1]$ conda config --add channels conda-forge
[skabdul@mn02 M1]$ conda config --add channels bioconda
[skabdul@mn02 M1]$ conda install -c bioconda circle-map
Fetching package metadata .............
Solving package specifications:
PackageNotFoundError: Packages missing in current channels:
- circle-map -> biopython >=1.73 -> libgcc-ng >=7.3.0
- circle-map -> numba >=0.43.1 -> libstdcxx-ng >=7.3.0
- circle-map -> numba >=0.43.1 -> llvmlite >=0.28.0
- circle-map -> pandas >=0.24.2
- circle-map -> pybedtools >=0.8.0
- circle-map -> scipy >=1.2.1 -> libgfortran-ng >=7,<8.0a0
- circle-map -> scipy >=1.2.1 -> openblas >=0.3.3,<0.3.4.0a0
- circle-map -> scipy >=1.2.1 -> libblas >=3.8.0,<4.0a0 -> blis >=0.5.2,<0.5.3.0a0
- circle-map -> scipy >=1.2.1 -> libblas >=3.8.0,<4.0a0 -> mkl >=2019.0,<2020.0a0
- circle-map -> scipy >=1.2.1 -> libcblas >=3.8.0,<4.0a0
- circle-map -> scipy >=1.2.1 -> liblapack >=3.8.0,<3.9.0a0
We have searched for the packages in the following channels:
- https://conda.anaconda.org/bioconda/linux-64
- https://conda.anaconda.org/bioconda/noarch
- https://conda.anaconda.org/conda-forge/linux-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.continuum.io/pkgs/free/linux-64
- https://repo.continuum.io/pkgs/free/noarch
- https://repo.continuum.io/pkgs/r/linux-64
- https://repo.continuum.io/pkgs/r/noarch
- https://repo.continuum.io/pkgs/pro/linux-64
- https://repo.continuum.io/pkgs/pro/noarch
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version 2.3.6
I have followed your instructions and try to use Circle-Map tool but it is showing error. Please tell me what's wrong with it.