When mapped to the genome and/or to the reference transcripts, RNA-Seq data can be summarized by a very large number of short-read counts. Accurate transcript quantification, such as gene expression calculation, relies on proper correction of sequence bias in the RNA-Seq short-read counts. We...
the paired-end RNA-seq data can be used to quantify gene expression and assess alternative isoform usage. The small RNA-seq data facilitates the exploration of multiple small non-coding RNAs, including miRNA, piRNA, snRNA, snoRNA, and tRNA. The miRNA expression data will be useful for understa...
(2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics Suppl. 14: S2.Zhao, Q.Y., et al. (2011). Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics, 12, S2. doi: ...
Yang Y, Smith SA (2013) Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics, 14, 328.Yang Y, Smith SA: Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics 2013, 14:328....
Here we present the RNA-seq consensus pipeline (RCP) developed by the GeneLab AWG along with the rationale behind the tool settings and options selected. The RCP includes three distinct steps: data pre-processing, data processing, and differential gene expression computation/annotation (Figure 1A)....
The Workhorse in NGS Labs: Short-Read Sequencing Short-read sequencing is a powerful tool for generating genomic data. With short read sequencing, DNA or RNA can be sequenced in a shorter amount of time and at a lower cost than traditional methods. This technology has revolutionized biomedical ...
(Fig.3d) after batch correction. Similar to the single-cell data, ST-HSC lied in between LT-HSC and MPP, corresponding to their biological status. Taken together, these results showed that the cells were correctly sorted and both the bulk and single-cell short-read RNA-seq data were of ...
Snakemake pipeline for detection & quantification of novel last exons/polyadenylation events from bulk RNA-sequencing data The workflow (in brief) is as follows, but can be toggled depending on your use case: Use StringTie to assemble transcripts from aligned RNA-seq reads Filter assembled transcrip...
Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas Advances in DNA sequencing technology have provided opportunities to produce new transcriptomic resources for species that lack completely sequenced genome... Mackenzie,R.,Gavery,... - 《Comparative Biochemist...
we report the analysis of two nanopore sequencing RNA-seq datasets with the goal of obtaining gene-level and isoform-level differential expression information. A dataset of synthetic, spliced, spike-in RNAs (“sequins”) as well as a mouse neural stem cell dataset from samples with a null muta...