I have this genome of a transposase from ciliate protozoa, i need to identify if the genome is from macronucleus or from micro nucleus, for that i have to know if it is from linear DNA or from circular DNA, how can i design an experiment for this genome sequence to know which nucleus it is from?
I only have this Genome sequences, from Ciliate cell, only the sequence is known,
Unless the macronucleus and micronucleus have distinct, known genome sequences (where checking alignment against that reference gives a unique hit), I don't really see how you could tell the source based upon the transposase gene sequence alone (unless there is some other aspect of ciliate biology that I don't understand).
Are the chromosomes unique enough for a clear alignment? I'm guessing this is with Illumina sequence data?
If you know the ends of the chromosome, you might be able use a structural variant caller (BreakDancer, SVDetect, etc.) to see if there are reads that cross between the ends of the chromosome.
However, you would also need to have the sample purely isolated from that one nucleus that you are testing (which seems like it could also have it's own set of technical issues, even if you were only working with linear DNA).
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Charles Warden
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