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adamewing / methylartist

Tools for plotting methylation data in various ways
MIT License
130 stars 10 forks source link

Question about output comprehension #78

Open VahidJavaran opened 5 months ago

VahidJavaran commented 5 months ago

Hi, Thanks a lot for your great package!! I used it and it worked very well with my samples. However, I could not understand some parts of results. Is there any document which explains each graph and its parameters and scales? For instance, I searched a lot to find what exactly below parts explain: image I would be appreciated if you have any suggestion or idea.

adamewing commented 5 months ago

Better documentation is on the to-do list, sorry, but if you have specific questions about that plot let me know what they are and also how the plot was generated.

VahidJavaran commented 5 months ago

Thanks @adamewing for your answer. I optimized my command line as you can see below:

methylartist locus -b ..._R1.bam,..._R2.bam,..._R3.bam -q 10 -r ...fasta -n CG -o ...svg --primary_only --plot_coverage ..._R1.bam,.._R2.bam,..._R3.bam --logcover --bed ....bed -i ..._isolate:0-3209 --mods m --samplepalette magma --svg --width 20 --height 10

now I want to know what are exactly each section of plot result. 6mA