RNA sequencing (RNA-seq) methodologies allow the discovery of novel variants and transcripts. These comprise three general steps: (1) capture of RNA species of interest, (2) conversion of RNA to complementary DNA (cDNA), and (3) modification of cDNA to fit the sequencing platform. Here we ...
SUPPA2 (v2.3) was used to analyze alternative splicing and differential alternative splicing:https://github.com/comprna/SUPPA seqkit (v2.1.0) was used to calculate the GC content of small RNA-seq data:https://github.com/shenwei356/seqkit ...
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 research and led to important discoveries in genomic...
Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics. 2013; 14 :328. doi: 10.1186/1471-2164-14-328. [ Cross Ref ]Yang, Y., & Smith, S. A. (2013). Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics, 14, 328....
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics. 2014;30:1660-6.Xie Y, Wu G, Tang J et al. (2013) SOAP... Yinlong,Xie,Gengxiong,... - 《Bioinformatics》 被引量: 632发表: 2014年 Optimizing de novo assembly of short-read RNA-seq data for ...
(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 ...
read specific tools for preprocessing together with established short-read RNA-seq methods. We usedlimma-voomto perform differential gene expression analysis, and the novelFLAMESpipeline to perform isoform identification and quantification, followed byDRIMSeqandlimma-diffSplice(withstageR) to perform ...
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression an... C Hyunghoon,D Joe,X Li,... - 《Plos One》 被引量: 26发表: 2014年 A comparison of short-read, HiFi long-read, and hybrid strategies...
Enormous databases of short-read RNA-seq sequencing experiments such as the NIH Sequence Read Archive (SRA) are now available. However, these collections remain difficult to use due to the inability to search for a particular expressed s... B Solomon,C Kingsford - 《Biorxiv》 被引量: 6发表...
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...