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Hi,
I'm trying to use `methpat` to visualize data generated with `bs-seeker2` as I was used to do with `bismark`. The input file is 'CpG_context_xxx.txt' from `bismark_methylation_extractor`, and it …
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Support that baseline can be fitted with either gene expression or protein abundance or methylation or … only
(or a combination of them?)
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I'm executing dorado on promethION flowcells while basecalling with super-accuracy and some methylations.
I'm running it per pod5 file, which I typically have 60-70 pod5 files per run.
Each pod5 fil…
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Hi,
I wanted to simulate some methylation treated reads, but all the reads are starting between position 1 and 10 of the reference genome.
Any suggestions?
Thanks
Fritz
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Hi Dinh,
I'm running your tool to extract methylation haplotypes from bam files, and I'm currently comparing the reads displayed in IGV with the methylation haplotypes generated from your tool. I'm…
caalo updated
6 years ago
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Hi,
My name is Alberto Rodriguez. Actually, I'm working with your package to analyze data coming from a epiGBS2 experiment using your protocol published in Biorxiv.
I have the following message …
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Hi,
I am interested in finding differentially methylated regions, and I have processed my PE-reads with Bismark.
I wanted to try DMRfinder to identify DMR, but I wanted to ask a question before mo…
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I have been using TEcount for estimating TEs in total RNA-seq data which has worked great. However, I want to combine this with methylation data and there we have methylation differences at the transc…
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Hello,
Thank you for creating minfi!
It is super useful!
Is there an hg38 version of an Illumina Human Methylation Array 450K annotation package?
Like this one: IlluminaHumanMethylation450kanno.…
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I started investigations into how to store such data in SAM. It's non trivial due to BAM's choice of using nibbles to store sequences, thus uppercase bases + ambiguity codes are the only choices avai…