Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols
In recent years, RNA-sequencing (RNA-seq) has emerged as a powerful technology for
transcriptome profiling. For a given gene, the number of mapped reads is not only …
transcriptome profiling. For a given gene, the number of mapped reads is not only …
[HTML][HTML] Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion
To allow efficient transcript/gene detection, highly abundant ribosomal RNAs (rRNA) are
generally removed from total RNA either by positive polyA+ selection or by rRNA depletion …
generally removed from total RNA either by positive polyA+ selection or by rRNA depletion …
[HTML][HTML] Evaluation and comparison of computational tools for RNA-seq isoform quantification
Background Alternatively spliced transcript isoforms are commonly observed in higher
eukaryotes. The expression levels of these isoforms are key for understanding normal …
eukaryotes. The expression levels of these isoforms are key for understanding normal …
The protein‐coding human genome: Annotating high‐hanging fruits
The major transcript variants of human protein‐coding genes are annotated to a certain
degree of accuracy combining manual curation, transcript data, and proteomics evidence …
degree of accuracy combining manual curation, transcript data, and proteomics evidence …
[HTML][HTML] JAFFA: High sensitivity transcriptome-focused fusion gene detection
NM Davidson, IJ Majewski, A Oshlack - Genome medicine, 2015 - Springer
Genomic instability is a hallmark of cancer and, as such, structural alterations and fusion
genes are common events in the cancer landscape. RNA sequencing (RNA-Seq) is a …
genes are common events in the cancer landscape. RNA sequencing (RNA-Seq) is a …
[HTML][HTML] A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification
Background RNA-Seq has become increasingly popular in transcriptome profiling. One
aspect of transcriptome research is to quantify the expression levels of genomic elements …
aspect of transcriptome research is to quantify the expression levels of genomic elements …
[HTML][HTML] Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap
Abstract Background While RNA-sequencing (RNA-seq) is becoming a powerful technology
in transcriptome profiling, one significant shortcoming of the first-generation RNA-seq …
in transcriptome profiling, one significant shortcoming of the first-generation RNA-seq …
[HTML][HTML] Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses subgenomic RNA
(sgRNA) to produce viral proteins for replication and immune evasion. We apply long-read …
(sgRNA) to produce viral proteins for replication and immune evasion. We apply long-read …
Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus
Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and
eQTL integration have predominantly employed microarrays to quantify gene-expression …
eQTL integration have predominantly employed microarrays to quantify gene-expression …
[HTML][HTML] Transcriptomic Analysis Provides Insights into Microplastic and Heavy Metal Challenges in the Line Seahorse (Hippocampus erectus)
Y Liu, D Shang, Y Yang, P Cui, J Sun - Fishes, 2022 - mdpi.com
Microplastics (MPs) are ubiquitous pollutants that have potentially harmful and toxic effects.
MPs are frequently ingested by aquatic animals, as microplastics share a similar size and …
MPs are frequently ingested by aquatic animals, as microplastics share a similar size and …