Comments (2)
asntech
commented on June 15, 2024
That is a lot of BED files! The memory issue is familiar with bedtools/pybedtools using large datasets. Can you use the latest versions of bedtools and pybedtools? Also, try to sort your bed files using bedtools before running the intervene upset.
We're aiming for a parallel processing option in the upcoming version of Intervene!
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alistairhockey
commented on June 15, 2024
I haven't had any issues with bedtools multiinter - but maybe the sorting has played a part in that!
Also, have you considered having an option for BEDPE files? I would be interested to see if you could modify the script to use 'pairToPair' in place of 'intersect' to get all the BEDPE paired region combinations.
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Related Issues (20)
- --bedtools-options doesn't work
- conda install not working with existing environment python=3.7 HOT 1
- search not working in readthedocs HOT 1
- error when attempting to use pairwise HOT 5
- total number diff in venn plot HOT 2
- Bedtools-options does not produce different results HOT 1
- upsetr script not plotting HOT 2
- Intervene venn –save-overlaps not working HOT 5
- Unable to install using conda HOT 5
- ipython-notebook not installing in conda HOT 4
- Intervene Docker HOT 2
- The intervene venn diagram is misleading HOT 3
- Support *.bedpe format
- --save-overlaps is not working HOT 1
- intervene pairwise: ValueError: keyword grid_b is not recognized; HOT 1
- Error in pairwise module HOT 9
- Differences between bedtools command line vs intervene pairwise? HOT 2
- Python 3.10 compatibility issues HOT 3
- Plotting crashed for small matrix with 0 and 1 HOT 1
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