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Hello,a few days ago I read a paper "MethylC-analyzer: a comprehensive downstream pipeline for the analysis of genome-wide DNA methylation" and I am trying to run the code "python MethylC.py command m…
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I'd like to be able to model data such as this:
-- whilst the sizes of the circles may be spot on there, the union/intersections relationships are way out of whack. I'd prefer to sacrifice the …
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Hi,
I wasn't clear from the documentation on the type of input file from WGBS data that it takes. Does it take BedGraph, a Bismark coverage file, or bed file?
Thank you very much,
Zo
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Hello,
As the data of WGBS is huge.
I have tested bismark for alignment. But it took lots of time.
Currently, like biscuit, bwameth can finish the alignment in more short time.
So, could cgmaptool…
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Thanks for your contribution, I want to refer to your process to implement it step by step, but I can't find the detailed use method, software and workflow,such as smtools、bismark、or piard???
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Hello,
I have Bed9+ files for WGBS and I wanted to estimate their ages. In the Bed9+ files, I have the beta values (in percentages) and the genome position rather than the CpG ID. Is there a way I …
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I tried calling SNPs in 64 WGBS samples. All failed with segmentation faults at various points. Can you walk me through how to provide you with the debugging information you need to fix this bug?
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Hi,
I am working with WGBS data from a triploid organism and would like to perform SNV calling using CGmapTools. The BayesWC strategy is based on the assumption of diploid genome. Would it be possibl…
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I installed using pip3. I am trying to run the CpG_aggregation.py test. I downloaded the test files, and am now running `CpG_aggregation.py -b hg19.RefSeq.union.1Kpromoter.bed.gz -i test_03_RRBS.bed …
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Hello, I tried to split the beta (hg19) of the cell_WGBS in the paper :
$ wgbstools segment --betas *beta --min_cpg 3 --max_bp 2000 -o blocks.small.bed
The following error occurred:
[wt beta] WA…