WebNov 23, 2024 · Splicing analysis from RNA-seq data Briefly, the MAJIQ build tool used the alignment BAM files from STAR along with a gene annotation file (GFF3) to define splice graphs and known/novel LSV. WebDec 1, 2024 · Differential splicing (DS) is a post-transcriptional biological process with critical, wide-ranging effects on a plethora of cellular activities and disease processes. To date, a number of computational approaches have been developed to identify and quantify differentially spliced genes from RNA-seq …
Improved methods for RNAseq-based alternative splicing …
WebSplicing done with MAJIQ tool still a work in progress The purpose of this pipeline is to be able to run MAJIQ using Snakemake. The aim is to make MAJIQ easier to run for non-bioinformaticians and it produces additional parsing and annotation to the MAJIQ output. I am actively developing how this pipeline works - for now it runs in 4 steps. WebNov 11, 2024 · Intron retention (IR) is a form of alternative splicing where an anticipated intron remains after transcript processing is complete. IR occurs in up to 80\% of protein-coding genes in humans [ 13] and may affect gene expression regulation [ 14, 15, 16, 17, 18, 19, 20] as well as response to stress [ 21, 22, 23 ]. gresh brebach
Splicing complexity as a pivotal feature of alternative exons in ...
Web13 hours ago · Alternative splicing of FGFR3 and CDK5RAP3 genes could also be observed upon the reduction of SRRM2 with an heterogeneous pool of siRNAs, suggesting that this was a direct consequence of lowered ... WebMay 1, 2024 · Overall, this work offers an outlier detection algorithm that can be combined with any splicing pipeline, a generalized and improved version of MAJIQ for DS … WebAug 13, 2024 · Alternative pre-mRNA splicing (AS) greatly diversifies metazoan transcriptomes and proteomes and is crucial for gene regulation. ... , share similar conceptual designs as JUM in which they utilize graphs of splicing junction clusters for splicing quantification. However, MAJIQ is not annotation-free and is still dependent on … fick\u0027s 1st law