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2.3 years ago
I have Brassica diploid and allopolyploid read sequence data with me. So I tried to align the raw reads using RSEM and it gives mapped read percentages below 50 (Although, I have changed the parameters and even used the defaults, it's still lower than 50%). Then, I used GSNAP for the read alignment of the same dataset and got the mapped read percentage around 90%. Does anyone has any idea why RSEM gives low mapping percentage?
