assembly.N25 | the number L s.t. 25% of all bases in the assembly are in a contig of length less than L. |
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assembly.N50 | the number L s.t. 50% of all bases in the assembly are in a contig of length less than L. |
assembly.N75 | the number L s.t. 75% of all bases in the assembly are in a contig of length less than L. |
assembly.longest | the length of the longest contig in the assembly. |
assembly.mean | the mean contig length in the assembly. |
assembly.median | the median contig length in the assembly. |
assembly.shortest | the length of the shortest contig in the assembly. |
assembly.num.contigs | the number of contigs in the assembly. |
Let A and B be assemblies or oraclesets. Let s be a contig in A and t be a contig in B. We define "s matches t" to mean that:
We define "num B in A" as follows. Let
C = \{(s, t)\in A\times B : s matches t\}.
Enumerate C according to the percent identity of s with t, and secondarily according to the negative of the percent insdel of s with respect to t. For each pair (s,t), if either s or t has already been seen earlier in the enumeration, throw out (s,t). Let "num B in A" be the cardinality of the remaining set.
The above definitions follow the Trinity paper.
We define "s matches t without checking insdel" to mean that there exists a contig t in B such that:
We define "num B in A without checking insdel" as above, but replacing "s matches t" with "s matches t without checking insdel".
num.oracleset.in.assembly | num oracleset in assembly |
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frac.oracleset.in.assembly | (num oracleset in assembly)/|oracleset| |
num.assembly.in.oracleset | num assembly in oracleset |
frac.assembly.in.oracleset | (num assembly in oracleset)/|assembly| |
num.oracleset.in.assembly.without.check.insdel | num oracleset in assembly without checking insdel |
frac.oracleset.in.assembly.without.check.insdel | (num oracleset in assembly without checking insdel)/|oracleset| |
num.assembly.in.oracleset.without.check.insdel | num assembly in oracleset without checking insdel |
frac.assembly.in.oracleset.without.check.insdel | (num assembly in oracleset without checking insdel)/|assembly| |
Let "s matches t" be as defined in the previous section. Let
C = \{t \in B : there exists s \in A such that s matches t\}.
We define "num B in A via allmatches" to be the cardinality of C.
Let "s matches t without checking insdel" be as defined in the previous section. We define "num B in A via allmatches without checking insdel" as above (for "num B in A via allmatches"), but replacing "s matches t" with "s matches t without checking insdel".
allmatches.num.oracleset.in.assembly | num oracleset in assembly via allmatches |
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allmatches.frac.oracleset.in.assembly | (num oracleset in assembly via allmatches)/|oracleset| |
allmatches.num.assembly.in.oracleset | num assembly in oracleset via allmatches |
allmatches.frac.assembly.in.oracleset | (num assembly in oracleset via allmatches)/|assembly| |
allmatches.num.oracleset.in.assembly.without.check.insdel | num oracleset in assembly via allmatches without checking insdel |
allmatches.frac.oracleset.in.assembly.without.check.insdel | (num oracleset in assembly via allmatches without checking insdel)/|oracleset| |
allmatches.num.assembly.in.oracleset.without.check.insdel | num assembly in oracleset via allmatches without checking insdel |
allmatches.frac.assembly.in.oracleset.without.check.insdel | (num assembly in oracleset via allmatches without checking insdel)/|assembly| |
rsem.approx.approx | I believe that this is the log model evidence, log P(D), computed using a convex approximation. |
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rsem.approx.bic | Log model evidence, log P(D), computed using BIC. |
rsem.approx.loglikelihood | I believe that this is the log likelihood, log P(D|\theta), computed at the MAP \theta. |
rsem.approx.loglikelihood.penalty | This is the BIC penalty. |
rsem.eval.lognumer.minus.logdenom | I believe that this is \log P(D|\theta') + \log P(\theta') - \log P(\theta'|D), where \theta' is a posterior mean estimate |
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rsem.eval.logprior | I believe that this is \log P(\theta') |
rsem.eval.loglikelihood | I believe that this is \log P(D|\theta') |
rsem.eval.logdenom | I believe that this is \log P(\theta'|D) |
rsem.prior.log.prob.M | This is \log P(M). |
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rsem.prior.log.prob.L.given.M | This is \log P(L|M). |
rsem.prior.log.prob.Sequences.given.L.and.M | This is \log P(Sequences|L, M). |
rsem.prior.log.prob.A | This is \log P(A) = \log P(M) + \log P(L|M) + \log P(Sequences|L, M). |
rsem.eval.loglikelihood.plus.rsem.prior.log.prob.A | This is \log P(A) + rsem.eval.loglikelihood |
rsem.approx.loglikelihood.plus.rsem.prior.log.prob.A | This is \log P(A) + rsem.approx.loglikelihood |
rsem.approx.approx.plus.rsem.prior.log.prob.A | This is \log P(A) + rsem.approx.approx |
rsem.approx.bic.plus.rsem.prior.log.prob.A | This is \log P(A) + rsem.approx.bic |
rsem.ss.mean.num.reads.per.transcript | Mean number of reads aligning to each transcript (based on countvs). |
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rsem.ss.median.num.reads.per.transcript | Median number of reads aligning to each transcript (based on countvs). |
rsem.ss.num.transcripts.with.zero.reads | Number of transcripts with no reads aligning to them (based on countvs). |
rsem.ss.num.matching.bases | Number of matching bases, based on the qpro profiles. |
rsem.ss.num.mismatching.bases | Number of mismatching bases, based on the qpro profiles. |