Abstract: The present invention relates to a set of oligonucleotides comprising index sequences and wherein the set comprises a plurality of subsets of oligonucleotides with different index sequences, wherein the index sequences of a subset of oligonucleotides differ at least by a non-zero number of sequence changes from each other; and wherein the set comprises at least 2 hierarchical tiers of subsets, wherein index sequences of a higher tier subset are members of a lower tier subset, and wherein the index sequences of a lower tier subset differ by a lower minimum number of sequence changes from each other than the index sequences of a higher tier subset; and wherein the oligonucleotides are assigned to one or more subsets. The invention further relates to methods of generating and using such sets.

Abstract: The invention relates to a method of estimating a nucleic acid copy number after amplification comprising the steps of providing a sample comprising nucleic acids of a to be determined number of copies; attaching variable labels to said nucleic acids; amplifying said nucleic acids with the labels with a nucleic acid duplication procedure, preferably PCR; determining amounts of amplified nucleic acid copies with a label, each amount is determined for nucleic acid copies with a different label; and providing an estimation of the nucleic acid copy number in the sample based on the determined amounts of amplified nucleic acid copies; as well as computer program products adapted for performing such methods.

Abstract: The invention relates to a method of estimating a nucleic acid copy number after amplification comprising the steps of providing a sample comprising nucleic acids of a to be determined number of copies; attaching variable labels to said nucleic acids; amplifying said nucleic acids with the labels with a nucleic acid duplication procedure, preferably PCR; determining amounts of amplified nucleic acid copies with a label, each amount is determined for nucleic acid copies with a different label; and providing an estimation of the nucleic acid copy number in the sample based on the determined amounts of amplified nucleic acid copies; as well as computer program products adapted for performing such methods.

Abstract: A method of estimating transcript abundances includes: (a) obtaining transcript fragment sequencing data from a potential mixture of transcripts of a genetic locus of interest; (b) assigning this data to genetic coordinates of the locus of interest to obtain a data set of fragment genetic coordinate coverage and a coverage envelope curve; (c) setting a number of transcripts of the mixture; (d) pre-setting a probability distribution function of modelled genetic coverage for each transcript i composed of the product of a weight factor ?i and the sum of at least 2 probability subfunctions j independently weighted by a weight factor ?i,j; (e) adding the probability distribution functions for each transcript to obtain a sum function; (f) fitting the sum function to the coverage envelope curve to optimize ?i and ?i,j to increase the fit; and (g) repeating steps (e) and (f) until a pre-set convergence criterion has been fulfilled.

Abstract: The present invention provides a method for determining an amount of nucleic acid molecule copies of a preselected nucleic acid molecule in a sample in a fragmentation based method, comprising the steps of providing the fragment amount for said preselected nucleic acid molecule, a distribution of fragment coverage over a genetic coordinate for said preselected nucleic acid molecule, obtaining a plurality of virtual fragments, assembling the obtained virtual fragments, obtaining the amount of assembled virtual fragments per assembled sequence, whereby the amount of the copies of a preselected nucleic acid molecule in a sample can be calculated from the fragment quantity and the amount of assembled virtual fragments per assembled sequence.