I have done miRNA sequencing and there are 464 novel miRNAs. How is it to show novel miRNAs on heat map, volcano plot along with known miRNAs?

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Ayaz Anwar

Volcano plot is the just the scatter plot between expression change (log2 FC) and the significance (p- value or adjusted p-value). So, if you have both values i.e. log2FC and p-value you can plot them using R or even excel.

https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html

What you want to show on heatmap, intensity, correlation or something else? If you have those values, you can create heatmap using ComplexHeatmap, pHeatmap or even ggplot2 (packages in R).

https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html

>Secondly, I also want to know how to go ahead with novel miRNAs?

Mehjabeen Javed

Do I have to show novel mature/precirsor miRNAs along with known miRNAs on heatmap, MA plot, PCA plot and volcano plot?

It depends on the design of your study, if those are important, you can show them, otherwise, no. You can create a PCA plot and see if they clustered together or search for their targets and see if their targets cluster together.

@Ayaz Anwar Could you please help me figure out what type of PCA plot is it...I obtained some random data. Is it normal to have such PCA PLOTS? How is it to show in publications?