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Hi, I have some WGBS data and would like to check the copy number variant in these data. However, I am not sure whether CNVkit is suitable for WGBS data since the methylated C is converted to T in WGB…
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I am having troubles with --methy-extract command.
I succeeded in generating *bmm files but I am having problems with understanding how to pass them properly as the option is not documented. Judging …
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Currently we have a limitation on the number of samples supported by bsseq, based on R limitations on the size of a matrix. This translates into ~85 samples with 26M CpGs. We need to address this.
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when the target vector is negative (i.e. negative fold changes), is.noCovNA gives wrong results - it converts all < 0 values to NA
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## [] std::bad_alloc
I'm trying to basecall my pod5 files on our linux remote server, but I keep getting the same std::bad_alloc error. The run starts but then shortly stops and all I get is an empty…
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hi,
I have a bunch of samples and trying to run nanopolish to extract DNA methylation. While I run two of the samples, nanopolish seems to encounter a problem. It cannot find the plugins to vbz. I…
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Below we consider new names for what to date we have been calling 'Sequence-Level Variation' vs 'Post-Sequence Variation', and for what to date we have been calling 'Precise Variation' vs 'Bucket Vari…
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I am currently working with minfi and I have a samplesheet where the idat files are not located in the base directory. I therefore adapted the code so I can specify multiple directories to the idat fi…
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Did you try a linear regression with Gaussian error on your processed data? Didn’t see any mention of such a model in the write up.
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### Contact Details
_No response_
### Scripts
03b-methylation_adjustment1.sh
### What happened?
03b-methylation_adjustment1.sh
resources/methylation/adjust_covs.R
modified the following:…