(2009) Transcript quantification with RNA-Seq data. BMC Bioinformatics, 10(Suppl 13), P5.Bohnert R., et al. (2009) Transcript quantification with RNA-Seq data . BMC Bioinformatics , 10 ( Suppl 13 ), P5.Bohnert R
RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification
quasi-mapping应用到的数据结构是:a combination of data structures—a hash table, suffix array (SA) and efficient rank data structure quasi-mappings的详情见:RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes #构建quasi-mapping-based index##注意,此处的-k值的...
RNA Integrity Number (RIN) is the most widely used approach to assess in vitro RNA degradation [1–3,7]. However, the RIN metric has several weaknesses that limit its applications in both pre-sequencing RNA sample screening and post-sequencing RNA-seq data analysis. First, the RIN score rel...
Context-aware transcript quantification from long-read RNA-seq data with Bambu Article 12 June 2023 Main The rise of long-read RNA sequencing (lrRNA-seq) technologies demands thorough evaluation. The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP), an open community effort modeled...
NanoString counts were compared to the highest RPKM value reported for transcript isoforms consistent with the probe design (correlation rc) or for any isoform from the locus (correlation ra). Source data Full size image Quantification of expression levels from RNA-seq data...
RNA-seq: impact of RNA degradation on transcript quantification. BMC Biol. 2014;12:42. 5. Sigurgeirsson B, Emanuelsson O, Lundeberg J. Sequencing degraded RNA addressed by 3′ tag counting. PLoS One. 2014;9:e91851. 6. Opitz L, Salinas-Riester G, Grade M, Jung K, Jo P, Emons G,...
Chen, Y., Sim, A., Wan, Y.K. et al. Context-aware transcript quantification from long-read RNA-seq data with Bambu. Nat Methods (2023).https://doi.org/10.1038/s41592-023-01908-w Contributors This package is developed and maintained byYing Chen,Andre Sim,Yuk Kei Wan,Keith Yeo,Min ...
A minimum of 8GB of RAM is recommended for running StringTie on regular size RNA-Seq samples, with 16 GB or more being strongly advised for larger data sets. StringTie options The following optional parameters can be specified (use -h or --help to get the usage message): --version : ...
Transcript assembly and quantification by RNA-Seq reveals.pdf,l e t t e r s transcript assembly and quantification by rNA-seq reveals unannotated transcripts and isoform switching during cell differentiation 1–3 4 2 4 4 5 Cole Trapnell , Brian A William