... I ran an mRNA seq analysis with three groups: control, treated1, treated2 - each with two replicates.
When I look at the comparison of 'treated2 vs control' I notice that most of the genes that hit statistical adjusted p-value are 'log2FoldChange' positive - meaning they are up-regulated in treated ...
... I have a 3-prime RNA seq library which I have analyzed using STAR aligner followed by Salmon counter and currently analyzing the data using DEseq2.
It appears that I am getting many counts for some genes.. and I assume this is since I have used a 3' lib in which most reads are concentrated in a sm ...
... I've searched around and could not find (possibly missed) advice on which transcript quantification tool is well suited for 3' prime RNA-seq lib?
I've considered using Salmon, but I'm not sure if it will correct for transcript length which is expected to be only a small part of the transcript
... Hello Biostars,
I have 10x SC expression data which I have processed using Seurat, and now I wish to test the association of several gene-sets with certain clusters. What approach/R package would you recommend?
I suppose I can run GSEA on the expression of individual cells, but next how do I summar ...
written 4 months ago by
roy.granit • 770
4 months ago by
igor ♦ 7.3k