Hello fellow researchers,
For my research I have acquired fragment size data for the analysis of microsatellites in Aspergillus fumigatus. I want to compare my data to other studies. wherein most data are represented in repeat numbers.
I have tried to convert the fragment size data by using the formula: Repeat number = Fragment size - (Forward primer length - forward spacer length)- (Reverse primer length - reverse spacer length) = X / repeat unit size.
However, I could not retrieve the spacer length from a reference A. fumigatus strain.
Can anybody help me further in finding a possible easier way to convert Fragment size to repeat number?
Thnx!
Dear Ervin Alcanzo ,
One way to convert fragment size data to repeat number is to use a reference strain of A. fumigatus that has been fully characterized in terms of its microsatellite repeat unit size and primer sequences. You can then use the known primer sequences and repeat unit size to calculate the repeat number for your own fragment size data. Additionally, you can use software such as Microsatellite Analyzer (MSA) or Tandem Repeats Finder (TRF) to align your fragment size data with the reference strain and predict the repeat number based on the alignment. Another approach would be to use a software such as PeakScanner that can automatically detect and score microsatellites from fragment analyzer data. This software can also be used to convert fragment size data to repeat number by taking into account the known repeat unit size and primer sequences. You can also check the publications of microsatellite studies on A. fumigatus, and find the primer sequences and repeat unit size used in those studies, and apply them in your own data. It is important to note that when comparing data from different studies, it is crucial to ensure that the primer sequences and repeat unit size used are the same or very similar to avoid any bias in the comparison.
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