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                                            Ren-Meng

Bowtie2 (2.5.1) reported very different alignment rates with and without --no-mixed --no-discordant

Thanks for your prompt reply~ Samples ENCFF763WUN and ENCFF658IDE (ENCSR769FOC) from ENCODE were used to perform this analysis. And I also used Bowtie2 (2.4.5) to align reads from this paired-end...