methplotlib
methplotlib copied to clipboard
wdecoster
Plotting tools for nanopore methylation data
Dear Wouter, I am getting the following error. The version of methplotlib I am using is **0.13.1**. Please help. methplotlib -m methylation_calls_CpG_sm1.tsv.gz methylation_frequency_sm1.tsv.gz -n calls frequencies -w mtDNA:1-16,626 -g /cluster/projects/nn9337k/as1_nanopolish/all_context/sequence.sorted.gtf.gz...
After some work I managed to use the github repo to get the right methplotlib version. However my bedmethylfile looks like this: 15 25685968 25685969 h 12 + 25685968 25685969...
Hello, I was trying out methplotlib, and my input data was a bedgraph file generated by Modkit. However, i am getting an input file not recognized message. Do you have...
Hi, I get an error as follow: 1, my command: ~/miniconda3/envs/OSCC/bin/methplotlib -m /NAS/wg_xialin/pancancer/raw_data/oral/fast5/yyl.T/yyl.T_methy.tsv /NAS/wg_hl/pancancer/OSCC/Methylation/f5c_meth/OSCC3/OSCC3.meth_cov10_freq.format.tsv -w chr1:99678000-99688500 -n calls frequencies --simplify error: Input file /NAS/wg_hl/pancancer/OSCC/Methylation/f5c_meth/OSCC3/OSCC3.meth_cov10_freq.format.tsv not recognized! Detailed error: Traceback (most...
Hi @wdecoster , This is not for error/issue. I am just wondering whether can I use the remora .bam file (MM/ML tag) as input. Also, I could not see the...
Hi @wdecoster I have 2 nanopolish output tsv files (calls and frequencies). I would like to use them as input for methplotlib. I have tried to sort as you wrote...
Hello, I am using megalodon to identify methylations in the whole genome, not only in the CpG islands. I was wondering if it is possible to use Methplotlib to visualise...
Dear Wouter, I am interested in using Methplotlib for visualizing m6A RNA frequencies and probability output by nanocompore. The Nanocompore SampComp function generated several files named "simulated_shift.tsv", "simulated_report.tsv" and so...
Hi again! I was trying to use Methplotlib to see if I can plot my Megalodon data for 6mA and 5mC. Simply converting my sorted BAM output using samtools to...
This allows users to run multiple analyses from the folder in which the Snakefile is located and the results from each will be put in different folder. They can also...
