What is your read-length distribution? The older versions of TopHat had problems, in case of too high length differences. Additionally, reads below 20 bp are very hard to map; I discard all reads below that length (denote you need to control for the pairing information).
Otherwise, you can try a different aligner (e.g. STAR or bbmap).
Otherwise, you can try a different aligner (e.g. STAR or bbmap).
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