rna seq - How can we distinguish between true zero and dropout …
Jun 13, 2017 · In single-cell RNA-seq data we have an inflated number of 0 (or near-zero) counts due to low mRNA capture rate and other inefficiencies. How can we decide which genes are 0 due to gene dropout (lack of measurement sensitivity), and which are genuinely not expressed in …
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 - What methods are available to find a cutoff value for non ...
Jun 13, 2017 · I have a gene expression count matrix produced from bulk RNA-seq data. I'd like to find genes that were not expressed in a group of samples and were expressed in another group. The problem of course is that not all effectively non-expressed genes will have 0 counts due to sequencing errors, or because they were expressed in a small subset of cells.
rna seq - Are mitochondrial genes to exclude in scRNA-seq such …
You might catch a few lucky ribosomal RNA (Rn45s) copies that were transcribed recently and still haven't been processed, but depending on your RNA-seq protocol, there's a chance they are acting as a functional part of the ribosome rather than an intermediate stage. $\endgroup$ –
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 ...
Why total RNA-seq usually yields low mapping rate?
Nov 22, 2017 · A likely explanation is that total RNA-Seq contains a high fraction of reads from ribosomal RNAs. Ribosomal RNAs are present in multiple copies across the genome, hence many reads map to multiple genomic locations and get discarded by the aligner.
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. And this won't effect any downstream analysis.
rna seq - What are common ways to calculate gene length for TPM ...
Apr 26, 2021 · My question is, given an annotation file of genes (for example from Ensembl here), how do you calculate gene length for the purpose of calculating TPM on a gene count matrix coming from RNA seq data. That is, I understand the actualy calculation of TPM given gene lengths, but I do not understand what the gene lengths are.
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.
rna seq - How to find adapter sequence - Bioinformatics Stack …
Oct 26, 2020 · The definitive answer is the sequencing institute/lab. They know what protocol/chemistry etc. was used. If you don't have access to that a number of tools check for known adapter sequences.