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FAQ.html
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<pre>
Q: What symbol should I use to indicate growth (+) and no growth (-)?
A: In order for gene conversion calculations to work, please use + for growth and - for no
growth. And in your parental genotypes, use + to indicate prototrophy and - to indicate
auxotrophy. For mating types, please use a for MATa and f for MATalpha.
Q: How do I indicate dead spores?
A: You should use either x or space.
Q: What’s the difference between “New tetrad data entry” and “Upload existing tetrad data”?
A: Use “New tetrad data entry” tab when you are getting started to setup your file and generate
the data table. You can then continue entering your tetrad data on the table generated. Use
“Upload existing tetrad data” when you have already entered some data using the “New tetrad
data entry” and saved the file on your disk. You can then upload that file and continue to
work on it. You can also upload an old file not generated by this app if you set it to the
same format as the app.
Q: Can I use the back button or the backspace key to go back to the last page?
A: No. You must click on the tabs to navigate through the app. Otherwise you progress will be lost.
Q: Are the files automatically saved?
A: The data you enter into the app data table are not automatically saved to your disk. So make
sure you use the download button to save a copy to your local drive. Also the idle time for
the server is 1 hour maximum, so save the file before leaving your computer for long periods.
Q: Can I save my file as .xls or .xlsx formats?
A: The default format saved is CSV file. You would need the CSV file for uploading to the app for
it to work. But after saving the CSV first, you can certainly open it in Excel and then save as
other formats if you’d like to.
Q: Can I add more markers after I have already created the table?
A: Yes, simply type additional marker names after the ones you have already entered in the box
provided and then hit submit again. Please note that if you have already entered some tetrad
data, they will not be preserved. However, the easiest way to add a new column is open the CSV
file in Excel and add a new column anywhere you want.
Q: Can I add more tetrads when I am using the “Upload existing tetrad data” tab?
A: There will be an “Add more tetrads” button on the left of the page once your table
has been uploaded.
Q: Where can I calculate interference?
A: The interference calculation is only available in the "Upload existing tetrad data" tab.
After you have uploaded a CSV file, the button "Interference (Malkova)" will appear.
Q: When I hit “Map distance", "Gene conversion frequencies", or "Interference (Malkova)"
button, where are the results?
A: You will be automatically redirected to the tab to show you the results. There is also a
"back to data table" button to go back to you tetrad data.
Q: Can I only analyze map distance of two markers but not all of them?
A: Yes. Use the dropdown menu above the table to select the genes you want to analyze. For map distance
you must select at least two genes. for gene conversion frequencies you much select at least one gene.
For interference, you must select at least three genes. The order of the genes will depend on the
order you click in the dropdown menu.
Q: What does the extract button do?
A: The extract button is to extract tetrad data based on the tetrad type of a reference interval that you
specify. This will out put a table containing either just NPD+T or PD of the reference interval and then
all the test interval data based on that information. If you wish to do interference (Malkova) manually,
you can extract the tables you want and then count the PDs, NPDs, and Ts.
Q: When I click on the buttons to calculate map distance, gene conversion or interference, nothing seems
to happen.
A: Sometimes when your tetrad data is large, it may take a few seconds to finish calculation. So please
be patient and wait for the results to appear.
Q: What is NPD ratio?
A: NPD ratio is the ratio between observed NPD proportion and expected NPD proportion of an interval. The
equation used to calculated expected NPD proportion is from Papazian 1952 genetics paper (PMID:17247384).
It is used to show whether there is interference in that interval. If the ratio is 1, then no interference.
If the ratio is less than 1, there is interference. If the ratio is greater than 1, there is negative
interference.
</pre>