Independently with analogous parameters, except that no new junctions were allowed (--no-novel-juncs), besides junctions, obtained on the first step, as recommended by the developers. Mapping options for GSNAP were as follows: --max-mismatches=0.07 --suboptimal-levels=2 --novelsplicing=1 --localsplicedist=50000 --pairmax-rna= 50000 --sam-multiple-primaries with the paired reads and singletons anal
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