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getScorePerBigWigBin.py error with output from bigWigMerge #1208
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perinom
changed the title
ComputeMatrix error with output from bigWigMerge
getScorePerBigWigBin.py error with output from bigWigMerge
Apr 5, 2023
I found a workaround:
This confirms that the incompatibility is with the output format of You can close this if you wish, but Thanks again for deeptools! |
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Hi, thanks for the amazing tools!
I'm having an issue with
ComputeMatrix
when providing bigwigs generated viabigWigMerge
.briefly, my pipeline is
Now, when I run ComputeMatrix on these merged bw I get
The starting bw pre-merge (generated with
bedGraphToBigWig
) are fine and run without complaints. Both pre-merge and post merge bw can be loaded in IGV w/o problems and look as they should.The only thing I noticed looking at the corresponding bedgraphs is that the pre-merge has a first line covering the chromosome from 0 to the first base with signal, while the post-merge start with signal regions from line one. as examples:
pre-merge
post-merge
Could this be sufficient to create problems? If so, is there a quick fix?
ComputeMatrix command
same error message across multiple python/deeptools combinations all in fresh, dedicated conda environments
deeptools 3.5.1
inPython 3.7.12
deeptools 3.5.1
inPython 3.9.15
deeptools 3.5.1
inPython 3.10.8
deeptools 3.4.3
inPython 3.9.15
Thanks!
------------------- EDIT ------------
updated title as the same issue happened with
multiBigwigSummary
and the issue seems to come fromgetScorePerBigWigBin.py
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