wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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Expectation Maximization on TE counting #100

Open AresRASP opened 6 months ago

AresRASP commented 6 months ago

Hi!

I am new to this software and I have been using it in my new project to quantify TEs because we are interested in the Expectation Maximization method. The first time I used the Count function, I specified the -e EM, but I obtained an error as if it didn't recognize EM as and option. Did I do it wrong?

So since if one does not specify anything it will be automatic, I left the default setting (so I did not add the -e argument). But how do I know if it was applied or not? Is there a file that should be the TE counts with EM or a column? Because in my results for some TEs I obtain the same number of counts (here below an image of an example), is that normal? Does it happen if the two elements are exactly the same?

Captura de pantalla 2024-05-17 a les 19 44 01

If is that: Is a distribution of the total counts between the 2 possible locus, or is the number of reads duplicated?

Thank you very much for your help.