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He reads was performed independently with TopHat v. 2.0.6 [52] and GSNAP v. 2012-12-20 [53]. In TopHat the following principal options were specified for mapping paired reads: --read-mismatches 7 --read-gap-length 2 --read-edit-dist 7 --mate-inner-dist 0 --mate-std-dev 100 --min-anchor-length 5 --min-intronlength 10 --max-intron-length 50000 --max-insertionlength 3 --max-deletion-length 3 --microe
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