Normalize and filter RNA-seq data
If I want to filter low expressed gene from my RNA-seq results, should do this before or after normalization by library size?
Many thanks
rna-seq
rna-seq
limma
• 3,006 views
•
link
written
by
Phoenix Mu
10
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
RNA seq normalization and gene gene correlation
written by Fish 0Hello, I'm new to RNA seq data and would like to seek your help in the following. My goal is to analyze gene-gene co-expression using …
-
filtering low expressed gene in microarray for WGCNA
written by Fluke 1Hi everyone I have 2 dataset, one is RNA-seq data from TCGA and another is microarray data. For RNA-seq, I filter low expressed gene and …
-
Filtering of low expressed gene in obtained from single cell line
written by bioinformatics.queries 7Hello Everyone I am having two biological replicates obtained from one cell line by RNA-sequencing. The alignment was done using STAR and counts were generated …
-
Statistically overrepresented gene types from Differentially expressed genes.
written by EVR 61Hi, I have DESeq2 results from RNA-seq after comparing Control and Treated samples and obtained a list of differential expressed genes(DEG). My DEG includes genes …
-
How to normalize gene expression with CPM
written by concetta 1Hi, I am analyzing RNA-seq data produced with 3' mRNA-Seq. I calculated gene counts using HTSEQ-count and I must normalize my counts to perform a …
-
Few SNPs after merging my samples with 1000G phase 3
written by Phoenix Mu 10I used pruned SNPs from 1000G phase 3 to do a PCA, and got the following results: ![enter image description here][1] In the plot above, …
-
Minimal TPM threshold for qPCR measure of gene expression
written by tlorin 37Hello, I am not a molecular biologist and I am mostly doing RNA-Seq. I want to find marker genes based on RNA-Seq results and I …
-
The RNA-Seq data input for WGCNA in terms of gene co-expression network construction
written by wangdp123 34Hi there, I am learning to use RNA-Seq data matrix with WGCNA to build up gene-co-expression network. I know WGCNA was designed for the microarray …
-
low expressed gene filtration, quantile normalization and log2 transformation, which one goes first?
written by ewre 26Hi everyone, I have been dealing with expression data for about 4 years (both microarray and rna-seq). but this question still confuses me when I …
-
A Basic question regarding lncRNA identification pipeline.
written by rajeev.vikram 4Hi, I have been analyzing RNA-Seq data sets of some Breast cancer cell lines to create a high confidence list of expressed lncRNAs. However as, …
This has been asked already today: RNAseq analysis: what comes first, filtering or normalization