For single end (based on trinity, oases, and collectContigs): [1] "correlation with rsem.eval.loglikelihood:" .id cor.with.rsem.loglik 1 assembly.N25 -0.7793712 2 assembly.N50 -0.7142805 3 assembly.N75 -0.7932991 4 assembly.longest 0.4718655 5 assembly.mean -0.7934438 6 assembly.median -0.7687059 7 assembly.shortest -0.5973121 8 assembly.num.contigs 0.4704803 9 num.oracleset.in.assembly 0.8512117 10 frac.oracleset.in.assembly 0.8512117 11 num.assembly.in.oracleset -0.3166736 12 frac.assembly.in.oracleset -0.4870214 13 num.oracleset.in.assembly.without.check.insdel 0.8512117 14 frac.oracleset.in.assembly.without.check.insdel 0.8512117 15 num.assembly.in.oracleset.without.check.insdel -0.3166736 16 frac.assembly.in.oracleset.without.check.insdel -0.4870214 17 rsem.approx.approx 0.9999973 18 rsem.approx.bic 0.9999906 19 rsem.approx.loglikelihood 0.9999999 20 rsem.approx.loglikelihood.penalty 0.4704834 21 rsem.eval.lognumer.minus.logdenom 0.9999973 22 rsem.eval.logprior 0.4616173 23 rsem.eval.loglikelihood 1.0000000 24 rsem.eval.logdenom 0.4689937 25 rsem.ss.mean.num.reads.per.transcript -0.7781437 26 rsem.ss.median.num.reads.per.transcript -0.6259166 27 rsem.ss.num.transcripts.with.zero.reads 0.4533496 28 rsem.ss.num.matching.bases 0.9986799 29 rsem.ss.num.mismatching.bases 0.6285869 For paired end (based on oases and collectContigs): [1] "correlation with rsem.eval.loglikelihood:" .id cor.with.rsem.loglik 1 assembly.N25 0.8979830 2 assembly.N50 0.8762195 3 assembly.N75 0.5694138 4 assembly.longest 0.9111307 5 assembly.mean 0.5748813 6 assembly.median 0.2808884 7 assembly.shortest -0.3501483 8 assembly.num.contigs -0.1373396 9 num.oracleset.in.assembly 0.9998119 10 frac.oracleset.in.assembly 0.9998119 11 num.assembly.in.oracleset -0.3001593 12 frac.assembly.in.oracleset -0.3019812 13 num.oracleset.in.assembly.without.check.insdel 0.9998119 14 frac.oracleset.in.assembly.without.check.insdel 0.9998119 15 num.assembly.in.oracleset.without.check.insdel -0.3059423 16 frac.assembly.in.oracleset.without.check.insdel -0.3070415 17 rsem.approx.approx 1.0000000 18 rsem.approx.bic 1.0000000 19 rsem.approx.loglikelihood 1.0000000 20 rsem.approx.loglikelihood.penalty -0.1373443 21 rsem.eval.lognumer.minus.logdenom 1.0000000 22 rsem.eval.logprior -0.1565712 23 rsem.eval.loglikelihood 1.0000000 24 rsem.eval.logdenom -0.1525116 25 rsem.ss.mean.num.reads.per.transcript -0.2491836 26 rsem.ss.median.num.reads.per.transcript -0.3386864 27 rsem.ss.num.transcripts.with.zero.reads -0.2364310 28 rsem.ss.num.matching.bases 0.9999989 29 rsem.ss.num.mismatching.bases 0.8695818