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tzhu-bio / cisDynet

An integrated platform for modeling gene-regulatory dynamics and networks
MIT License
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How to get the PMW format text #9

Open linfanxiao opened 1 month ago

linfanxiao commented 1 month ago

Dear developers,

I found that there needs a PWM format text as input in the config file. However, Jaspar only provides PFM text and the R library construct a PWMatrixlist how to get the PWM format text we need in the snakemake pipeline？

Motif file with PWM format.

motif: /mnt/public3/cat/data/ATAC/jaspar.moitf.txt https://tzhu-bio.github.io/cisDynet_bookdown/book/snakemake-pipeline.html#config-file Linfan Xiao

tzhu-bio commented 1 month ago

You can download PFM (Single batch file) directly from jaspar data. Then import it directly into cisDynet snakemake.

linfanxiao commented 1 month ago

Thanks~

linfanxiao commented 1 month ago

Sorry, I have another question about 7.4 Compare the three samples' chromatin accessibility (Three samples). https://tzhu-bio.github.io/cisDynet_bookdown/book/differential-ocr-analysis.html#compare-the-three-samples-chromatin-accessibility-three-samples if we can use them in three groups (three biological replicates )or must use Chapter 8 Tissue(Sample) Specific Analysis (SPM methods)?

tzhu-bio commented 1 month ago

If you want to plot ternary diagrams, then you can only merge your biological replicates (e.g. take the average) before using the getTriads function.

If you want to show all replicates , you can choose the heatmap (like Chapter 8 Tissue(Sample) Specific Analysis).

linfanxiao commented 1 month ago

Thank you for your prompt and gracious response!