I am confused about the genes at the top of the volcano plot. There are a lot of genes at the top, what's wrong with it? If that's normal what's the interpretation of it?
I used volcano plot tools from galaxy with p-value=0.05.
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$\begingroup$ I suggest you give some background information about this plot as well as part of the data and the code that generates this plot. Asking this question without providing more information would be hard for us to help you. At first, I would say that you should set the Y axis to a higher value. $\endgroup$– user324810Sep 10, 2021 at 12:55
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$\begingroup$ thank u @Law for your comment, for the data I have three replicate of each condition, two conditions: treated and control, in a total: 12 samples in fastq format. i used this pipeline : Trimmomatic -> Kallisto -> Deseq -> volcano plot in galaxy $\endgroup$– ZahraeSep 11, 2021 at 13:15
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$\begingroup$ paired-end reads * $\endgroup$– ZahraeSep 11, 2021 at 13:35
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Either your graph or your data is capped at 300. Probably the p-values themselves; whatever calculated those p-values literally can't represent a number tinier than 1x10^-300
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$\begingroup$ thank u @swbarnes2 After trimming the quality of the data is good, there are no adapters or overexpressed sequences. for the alignment, I used Kallisto, then deseq for differential analysis. I tried to augment the max of the axis of the plot, but the top is 300. so us result we can't accepte this result ? The analysis will have to be redone ? $\endgroup$– ZahraeSep 11, 2021 at 13:34
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$\begingroup$ If the top is 300, you have to look for another galaxy website where the configuration of the volcano plot is more flexible. Or you can plot it manually with R. There are many websites that teaches you how to do a volcano plot. But what is intriguing to me is having a -log10 of more than 300... this seems excessive to me but it all depends on the research you are doing. $\endgroup$ Sep 11, 2021 at 20:45