I have been running a MAGeCK test command on the terminal for a CRISPR screen to rank sgRNAs and genes based on the read count tables. However, I get only the plot of the top-ranked genes (positively selected) but not the negatively selected ones. On the terminal, I get this error:
INFO  @ Mon, 29 Jul 2024 11:17:57:   Error in plot.window(...) : Logarithmic axis must have positive limits
INFO  @ Mon, 29 Jul 2024 11:17:57:   Calls: plotrankedvalues -> plot -> plot.default -> localWindow -> plot.window
INFO  @ Mon, 29 Jul 2024 11:17:57:   In addition: Warning message:
INFO  @ Mon, 29 Jul 2024 11:17:57:   In xy.coords(x, y, xlabel, ylabel, log) :
INFO  @ Mon, 29 Jul 2024 11:17:57:     1 y value
I found the solution to the issue. The problem was caused by a small formatting error in the gRNA list file. Specifically, there was a space between the gene name "septin" and the number "5" in the entry for "septin 5". It should be "septin5" without a space. This minor formatting error prevented the data from being processed correctly, leading to the plotting error. It took a long time to identify this issue, but it's resolved now. I'm sharing this in case someone else runs into the same error.
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