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Hello
Thanks for this great tool
I am running your differential methylation pipeline, following `modkit pileup` to call methylated sites. This is a plant genome so I have methylation in CG, CHG …
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Hi @al2na, I wanted to inquire if MethylKit package can be used to run Differential methylation analysis for methylation call data obtained from hifi reads.
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Beginning with sequence-based searches of the literature via PaperBLAST and using the sequences acquired from PomBase, UniProtKB
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Hello Sir
I using methylation calling on my 10-13X ONT datasets. I filtered methylaltion calls with log_like_ratio >=2 and >0 and then calculated methylated frequency on filtered methylation calls…
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In each condition, perform [Binding and Expression Target Analysis](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4135175/) (BETA) analysis to integrate DMR and DEG data. Also identify genes with expre…
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Hi,
I generated some input data with Bismark, with the following code:
`bismark_methylation_extractor -p --scaffolds --bedGraph --buffer_size 40G --genome_folder /home/juaguila/Bismark/ --cytosine_r…
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Data here: https://gannet.fish.washington.edu/metacarcinus/Cgigas/shelly/
First step is probably ensuring that there are BEDfiles for each data type (ATAC-Seq, csRNA-seq, 5'GRO, mSTART).
Next ste…
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Hello, I am not sure if this is the place to comment, but I have been trying to contact someone who could shed some light as to how solve this problem.
I have upgraded my R version as it kept prom…
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This issue will collect all feedback submitted via the feedback form at the end of each tutorial
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Results have been [aggregated](https://nbviewer.jupyter.org/github/bebatut/galaxy-training-m…
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Hi,
I'm running command "pycometh Meth_Seg" and encountering an error:
OSError: Unable to open file (unable to open file: name = '[/NAS/wg_hl/pancancer/OSCC/Methylation/f5c_meth/pycoMeth/MetH5/OS…