Recently I notice that the new version of Tophat does not output the read pairs which map to two different chromosomes. However, these alignments are outputted by old version. Does anyone know an option to get them out from the new Tophat?
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That is a bit scary. I wonder if this is a design shift with the introduction of tophat-fusion which is design for this issue. More I'm worried that a wierd cufflinks abundance issue with more "FAIL" genes might be related to a tophat error not cufflinks. Time for a matrix comparison of previous and current tophat version with previous and current cufflinks versions.
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