We are analyzing https://link.springer.com/article/10.1186/gb-2011-12-3-r22.

Title:
Improving RNA-Seq expression estimates by correcting for fragment bias | Genome Biology
Description:
The biochemistry of RNA-Seq library preparation results in cDNA fragments that are not uniformly distributed within the transcripts they represent. This non-uniformity must be accounted for when estimating expression levels, and we show how to perform the needed corrections using a likelihood based approach. We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies.
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Keywords {🔍}

bias, expression, correction, figure, rnaseq, pubmed, data, article, transcripts, fragment, file, transcript, correlation, google, scholar, estimates, parameters, fragments, read, additional, model, methods, sequencing, experiment, qrtpcr, sequence, central, estimation, positional, sra, dataset, length, analysis, results, authors, cas, method, protocols, reads, comparison, likelihood, based, protocol, due, content, full, rna, distribution, counts, isoform,

Topics {✒️}

sequence-specific bias profiles article number r22 rna-seq-based transcript quantitation article download pdf paired-end rna-seq data color-coded probe pairs taqman qrt-pcr probes rna-seq analysis pipeline conserved multi-exonic structure lior pachter rna-seq expression estimates rna-seq analysis approaches early rna-seq data cell type-specific transcriptomes /gf/project/wtpe/] trapnell expected read count differential expression analysis author information authors independently obtained qrt-pcr short read archive typical rna-seq experiment qrt-pcr expression data sequence count data maqc qrt-pcr data independently performed qrt-pcr paired-end read mappings count-based methods rna-seq analysis privacy choices/manage cookies rna-seq protocols improve gene expression measurements short-read rates full size image sequence-specific bias correction distributed open source rna-seq technology human rna-seq ncounter prep station correct --library-type option methods parameter estimation ncounter digital analyzer normalized nucleotide frequencies global transcription profiling raw expression estimates article roberts rna-seq data nucleic acids research rna secondary structure rna-seq leads validate rna-seq

Schema {🗺️}

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         description:The biochemistry of RNA-Seq library preparation results in cDNA fragments that are not uniformly distributed within the transcripts they represent. This non-uniformity must be accounted for when estimating expression levels, and we show how to perform the needed corrections using a likelihood based approach. We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies.
         datePublished:2011-03-16T00:00:00Z
         dateModified:2011-03-16T00:00:00Z
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            Positional Bias
            Read Count
            Differential Expression Analysis
            Bias Parameter
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      headline:Improving RNA-Seq expression estimates by correcting for fragment bias
      description:The biochemistry of RNA-Seq library preparation results in cDNA fragments that are not uniformly distributed within the transcripts they represent. This non-uniformity must be accounted for when estimating expression levels, and we show how to perform the needed corrections using a likelihood based approach. We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies.
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         Bias Correction
         Positional Bias
         Read Count
         Differential Expression Analysis
         Bias Parameter
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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