5' and 3' bias in Rna-seq data - Bioinformatics Stack Exchange
Feb 19, 2018 · I'm working with rna-seq samples. I see 5' bias and also 3' bias in the per-base sequence content plot. From this link I see that the bias at the start of the sequences appears to be the result of biased selection of fragments from the library.
RNA-Seq: clustering/treatment of genes with low expression
Aug 16, 2018 · I have some RNA-Seq data from leukaemia patients. I want to do unsupervised clustering on them with some other published leukaemia RNA-Seq data and see how they cluster. There are a few problems I encountered while doing this.
differential expression - What does an FDR value of 1 in RNA-seq …
Dec 3, 2018 · FDR stands for False Discovery Rate.It is a statistic tool used in multiple hypothesis testing. As you may know, when you use a p-value cutoff (usually 0.05) for your experiments, it means strictly speaking that "is there was actually no …
rna seq - Are mitochondrial genes to exclude in scRNA-seq such …
According to this, I think that mtRNA levels relative to endogenous RNA can be used as a control for low quality (broken) cells, in a similar way to ERCC spike-ins. Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC, Teichmann SA. Classification of low quality cells from single-cell RNA-seq data.
rna seq - Removing PCR duplicates in RNA-seq Analysis
Aug 18, 2017 · For normal RNA-seq PCR duplicates are normally kept in, but the duplication rate can be used as a quality control: The higher the duplication rate, the lower the quality. For expression analysis, it is probably best to discard high duplication rate samples, rather than deduplicate them.
rna seq - RNAseq: Z score, Intensity, and Resources
Jul 29, 2017 · However, this presents a problem. Most of the procedures we use in standard gene expression analysis involve comparing one group to another after suitable normalisations of the data. But here we have no suitable comparison group. To get around this problem in cancer RNA-seq analysis we do something called outlier detection.
rna seq - How to calculate fold change in gene expression from …
Mar 6, 2020 · You should use a proper statistical framework for RNA-seq dfferential analysis (which includes FC calculation). Standard tools for this are (among others) edgeR or DESeq2. You could use tximport to import RSEM outputs into R and then use its output for e.g. DESeq2. The linked manual provides example code for this.
rna seq - How to quantile normalization on RNA seq counts ...
RNA-seq: How to get new expression count after normalization. 1. What is a good RNA seq normalization ...
rna seq - Negative binomial modeling of RNA-Seq data
A common way to model RNA-seq data is using a negative binomial distribution, where each sample-gene pair ...
data storage requirements for RNA-seq and WGS
Jan 23, 2019 · Supposing upcoming RNA-seq for 3 conditions and 3 replications for each, how much is data storage requirements