I'm running tophat for Arabidopsis RNA seq samples.
I've performed 2 runs; one with -x 20 (default) and the second time with -x 1, with the goal of using only uniquely mapped reads.
My question is; in which of the many reports inside the "logs" output folder should I look in order to compare between the 2 runs. So many reports I got confused, I can only see that the BAM files of the second run are smaller in size, as expected ????
Tanks
Inbar
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