WebMar 30, 2014 · Ballgown provides improved statistical significance estimates as compared to the Cuffdiff2 differential expression tool included with Cufflinks. We demonstrate the flexibility of the Ballgown package by re-analyzing 667 samples from the GEUVADIS study to identify transcript-level eQTLs and identify non-linear artifacts in transcript data. Our ... WebFeb 21, 2024 · However, it remains unknown whether CD4 + thymocytes act exclusively on mature Aire + mTEC hi or upstream on their TAC-TEC precursors contained in mTEC lo and whether the development of the newly identified Fezf2 +, post-Aire, and tuft-like subsets is regulated or not by CD4 + thymocytes.
DESeq versus CuffDiff2 for RNA-seq expression quantification in ...
WebMay 30, 2014 · They observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives. Overall, DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study. WebNational Center for Biotechnology Information impact of it act
Thymocytes trigger self-antigen-controlling pathways in ... - eLife
WebJun 10, 2024 · 60 than DESeq and Cuffdiff2 in terms of its ability to detect true positives and recommended that 61 Cuffdiff2 should not be used if sequencing depth is low (i.e. <10 million reads per individual 62 sample). 63 Furthermore, most DGE analyses have been limited to designed experimental studies (eg. treated WebMar 6, 2015 · The P-value histogram for the latest Cuffdiff2 version (2.2.1) also revealed a signal (Supplementary Fig. 4), which is an improvement compared with earlier versions … WebTopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort among Daehwan Kim and Steven Salzberg in the Center for … impact of it on accounting