What is a common number of cells per cell type in single cell RNA Seq?
Jan 8, 2024 · Good afternoon, I just started working with Single cell RNA Seq and I am trying to understand what is an average / possible number of cells per sample. I am looking at a dataset of 7 …
enrichment of Mitochondrial genes in bulk RNA-Seq
Sep 23, 2025 · I performed RNAseq comparing two different populations of CD8+ T cells (from within the same donors.). The most differentially expressed genes in one group consists of mitochondrial …
5' and 3' bias in Rna-seq data - Bioinformatics Stack Exchange
Feb 19, 2018 · 6 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 …
differential expression - What does an FDR value of 1 in RNA-seq mean ...
What does an FDR value of 1 in RNA-seq mean? Ask Question Asked 7 years, 5 months ago Modified 7 years, 5 months ago
rna seq - RNAseq biological replicates not clustering in PCA plots ...
Jul 23, 2020 · I have RNAseq data from 4 samples with 3 biological replicates per sample. I am currently trying to do the differential expression analysis with DESeq2 but the biological replicates will not cluster
rna seq - The confusion of using TPM (transcripts per million ...
Nov 2, 2021 · For scRNA-seq, you don't want to normalize for gene length because the most popular 10X technology only sequences a the 3' or 5' end of the transcript. Hence CPM, which normalizes for …
rna seq - STAR quantMode vs RSEM vs Kallisto - Bioinformatics Stack ...
STAR quantMode (GeneCounts) essentially provides the same output as HTSeq-Count would, ie. number of reads that cover a given gene. This is the most simple measure of expression you could …
rna seq - Featurecount output .txt file from bam file - Bioinformatics ...
Jan 24, 2024 · rna-seq gene-expression read-mapping featurecounts Improve this question edited Jan 25, 2024 at 14:44 asked Jan 24, 2024 at 17:57
rna seq - HISAT2: RNA strandedness - Bioinformatics Stack Exchange
Nov 2, 2023 · Kind of a bad move to not have a way of explicitly recreating the default behavior. There should be an option you can pass to rna-strandness that replicates not specifying that parameter at …
rna seq - Difference between CPM and TPM and which one for …
Aug 15, 2017 · What the difference between TPM and CPM when dealing with RNA seq data? What metrics would you use if you have to perform some down stream analysis other than Differential …