Why total RNA-seq usually yields low mapping rate?
Nov 21, 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 …
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 …
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 …
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 …
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 …
rna seq - The confusion of using TPM (transcripts per million ...
Nov 2, 2021 · When I analyzed sc-RNA seq data, the Seurat package uses normalized counts (which is CPM) for DEG, but TPM is not advised for differential testing. I'm not sure what I'm …
rna seq - Reads mapped to exonic, intronic and intergenic regions ...
I would expect at least 30% of reads from a total-cell, ribo-depleted RNA-seq to be exonic. Less suggests something when wrong. As well as degradation, another explanation would be …
rna seq - TPM or rlog(CPM) for comparing expression?
I want to see the expression of a gene in a group of patient amongst the entire cohort using my RNA-Seq data. While I can do a differential expression analysis with limma or DESeq2, I want …
rna seq - What are the right parameters to trim a small RNA ...
Jul 14, 2019 · Steps that should always fail in RNA-seq: per-base sequence content (there's "random priming" performed that isn't completely random, so the first ~8 bases show a typical …
rna seq - Advantages of paired-end sequencing compared to …
Sep 12, 2020 · rna-seq; See similar questions with these tags. Featured on Meta Changes to reporting for the [status ...