methylpy
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yupenghe
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
DMR
Dear yupenghe, Why DMR does not need to distinguish +/- strand like DMS ? Thanks.
Dear yupenghe, I would like to know whether methylpy can be used for methylation analysis of plant genome because the results I get using methylpy are quite different from those...
Dear yupenghe, I would like to know to deal with organisms that have chromosomes more than 512Mb. During mapping, samtools index command failed with showing the error message. `samtools index:...
Hi, we are working on a BS-Seq benchmarking project and would like to ask your help in tuning the parameters of methylpy. If you can help, please get in touch...
Hello! I was wondering if `methylpy` methylation calling takes care of directional and non-directional libraries? To quote Bismark User guide here > Bisulfite treatment of DNA and subsequent PCR amplification...
Hello, I wonder if methylpy can filter reads by the methylation level of HCH. Because I have some NOMe-seq data，however they appeared to have low bisulfite conversion rate. I want...
Hello, I recently wanted to use methylpy to calculate DMR, I processed my methylation data into the allc file format,： > 8 7524770 + CTCGC 15 15 1 8 7524782...
Hi Yupeng, I am getting some strange error for cutadapt (3.4) after upgrading methylpy from 1.4.2 to 1.4.6. Here is the error message: ``` cutadapt: error: unrecognized arguments: -f x_libA_split_4...
When I run add-methylation-level with an input tsv (genes that are differentially expressed, for which I'm interested in getting total methylation level) methylpy generates a blank output file.
Dear Yupeng, Methylpy output showed a low rate of uniquely mapping read pairs: ``` There are 258651069 total input read pairs Wed Dec 25 08:40:05 2019 There are 15891937 uniquely...
