Different mapping rate for tophat+mm9 vs star+mm10

Question

[Ice P]

I recently switched from tophat+mm9 to STAR+mm10. I used pair end reads and default parameters for both cases. However I noticed that the percentage of uniquely mapped reads decreased significantly. Earlier mapping for different samples were around 80-90,; now decreased to 50-70%. Has anybody had similar experience? What could be possible reasons?

[Devon Ryan]

It's incredibly unlikely that STAR will produce fewer alignments than tophat, STAR is generally superior in all ways. Are you sure you're comparing the right numbers? Are you determining the percentages from the original number of reads or from the number of reads that align?