Web16 Jan 2024 · This is an expedient method that makes it practical to analyze the large volume of data produced by high-throughput sequencing. Reference-based methods also have costs. When the genome of a sample... WebHere, we will present BBMap [1], a fast splice-aware aligner for short and long reads. We will demonstrate that BBMap has superior speed, sensitivity, and specificity to alternative high-throughput aligners bowtie2 [2], bwa [3], smalt, [4] GSNAP [5], and BLASR [6]. For improved accessibility of PDF content, download the file to your device.
ASimulatoR: splice-aware RNA-Seq data simulation
WebWith only a genome, you must use a splice-aware aligner like BBMap. Theoretically, you can get better results (assuming optimal quantification postprocessing) when aligning to the genome compared to the transcriptome; but in practice it's not all that important because there is no current program that does a good job of quantifying gene isoform expression … Web23 Oct 2024 · Splice-aware RNA-seq alignment tools can be divided into two groups. First, guided splice-aware aligners, use the genome sequence and known gene annotations to … displays 2 go tracking
Alternative splicing analysis benchmark with DICAST - bioRxiv
Web4 Feb 2016 · It's only one caveat, though, because splice-aware aligners encounter the same problems. If you align to a genome, which I always recommend, splice-aware aligners are … Web7 Apr 2024 · Splice aware aligners take into account the splice junctions between exons in gene regions while aligning RNA-seq reads. So if a read spans the splice junction on either side, it gets aligned as such. In ungapped alignment, the splice junction would indicate only a partial match for the reads that span these junctions and it might not be aligned. Web23 Oct 2024 · Splice-aware RNA-seq alignment tools can be divided into two groups. First, guided splice-aware aligners, use the genome sequence and known gene annotations to calculate gene or transcript abundance, but cannot be used to identify new splice junctions. Second, de novo splice-aware aligners can align RNA-seq reads to a reference genomic … displays 2 go website