Recently started with ref based txome. i got the human data (5 samples, ~10M PE reads). Did the tophat and cufflinks and got the transcripts for each samples. What i observed is, all the samples have exact same number of transcripts (~40k). Just to check i tool another set (4 samples) of human samples, same result but this case ~43k transcripts. Same thing happened when i tried with mouse samples. My concern is, when i worked with plant sample i got different transcript numbers. In all cases none of the samples are replicates.
Q: Is this kind of consistency is normal. If so What went wrong in plant case. (All reference data was downloaded from ensemble)
Any suggestions are appreciated.