Tag: TPM

Accepted drop-seq 2.5.1+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sun, 16 Jan 2022 16:45:58 +0100 Source: drop-seq Architecture: source Version: 2.5.1+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Andreas Tille <ti…@debian.org> Changes: drop-seq (2.5.1+dfsg-1) unstable; urgency=medium . * New upstream version * Add missing build dependency…

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r – ggplot: Try to plot boxplots with geom_rect on its background, but keep having error with object “variable” not found

I was almost desperate with this error after working on this for 4 hrs, googled and looked from past posts already. Here is my data structure: str(tcga_exp) ‘data.frame’: 11775 obs. of 5 variables: $ cohort: chr “BRCA-Basal.Tumor” “BRCA-LumA.Tumor” “BRCA-LumB.Tumor” “BRCA-LumA.Tumor” … $ exp : num 6.35 5.54 6.56 5.05 5.98…

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Help needed for Ensembl Gene ID conversion for RNA-seq data

Hello All, I am new to the RNA-seq world and especially new to the bioinformatics side. We recently completed a RNA-seq experiment (total RNAs) on human samples and we used illumina’s Dragen RNA pipeline which generated salmon gene count (.sf) output files. In the files, the gene ID is in…

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Using machine learning methods to find a biomarker panel to diagnose a disease.

Hello Biostars. I obtained DEGs from RNAseq analysis for normal and infected samples. Then I decreased the number of them by some downstream analysis. Now I have 120 DEGs and I want to select between them the best combination of biomarkers that can recognize normal from infected samples (biomarker panel)….

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Statistics on RNAseq data

Statistics on RNAseq data 2 Hi I would like to know whether you can do statistical tests (e.g. ANOVAS etc.) on the TPM/RPKM counts of RNAseq data? Thanks on Statistics data RNAseq • 58 views This is not recommended due to a few underlying problems with RNA-seq data that include…

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Different Gene Lengths and Expected Gene Lengths from Sample to Sample

Different Gene Lengths and Expected Gene Lengths from Sample to Sample 0 Hi all, I have come across something I have never seen before. I am working with some data from an outside source which appears to be processed RNA-seq files. Like other processed RNA-seq files I have ran into…

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Transcriptional noise detection and Salmon TPMs

Transcriptional noise detection and Salmon TPMs 1 Hello, I’m analysing RNA-seq data from two datasets (from healthy samples) and created a unique GTF file to identify new isoforms by using StringTie. Then I used Salmon to estimate their TPMs, but I have some questions hoping anyone can help me: 1)…

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CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis | BMC Genomics

CeTF is an C/C++ implementation in R for PCIT [6] and RIF [7] algorithms, which initially were made in FORTRAN language. From these two algorithms, it was possible to integrate them in order to increase performance and Results. Input data may come from microarray, RNA-seq, or single-cell RNA-seq. The input…

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DESeq2 with a small number of genes

DESeq2 with a small number of genes 1 Dear all, I am writing a program in order to study the coverage of only one sequence. To sum up the pipeline: Detect ORFs in the input sequence Align all reads on the sequence (bowtie), reads come from RNA-seq Count the number…

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Whether the probe intensity of microarray can be used to calculate TPM like the count data of RNAseq?

Whether the probe intensity of microarray can be used to calculate TPM like the count data of RNAseq? 1 Hello everyone! I’m using a software that requires TPM. But I can’t find enough RNAseq data to do analysis at the moment. I have downloaded some microarray data from a database…

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Calculate TPM values from DESeq2 normalised counts

Calculate TPM values from DESeq2 normalised counts 0 Hi all! Still somewhat new to handling transcriptomic data, and have a newbie question. I’m just trying to convert some RNA-Seq count data to TPM for the purpose of presenting qualitative comparisons about relative expression of various genes in a single cell…

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When importing my quant.sf files into R using tximport, should I set ‘ignoreTxVersion’ to True or False?

Hello, I’m working through my first batch of RNA-Seq analysis and unfortunately I don’t have an experienced bioinformatician to work with. My question is regarding tximport of my quant.sf files into R. I have been working with the EquCab3.0 reference transcriptome from NCBI to generate these quant.sf files, but I…

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How does miRdeep2 normalise sequences

How does miRdeep2 normalise sequences 1 Hi, I have mirdeep2 output that looks like this. #miRNA read_count precursor total seq seq(norm) mmu-let-7a-5p 43271 mmu-let-7a-1 43271 43271 7658.26 mmu-let-7a-1-3p 784 mmu-let-7a-1 784 784 138.76 mmu-let-7a-5p 43224 mmu-let-7a-2 43224 43224 7649.94 I think using the seq(norm) would be appropriate, but I cannot…

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Gene co-expression in single-cell RNA-seq

Gene co-expression in single-cell RNA-seq 0 I am using single-cell RNA-seq data from the Allen Institute, and I want to look at gene co-expression in different cell populations. They provide raw UMI counts, so I’m wondering what normalization method to use (e.g., CPM, TPM, VST) to look at these correlations….

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Normalisation for single nuclei RNA-seq

Normalisation for single nuclei RNA-seq 0 For single cell RNA-seq the typical workflow includes a normalisation step to account for variable sequencing depth. In Scanpy/Seurat, CPM (Counts per million) is a simple and common choice. We don’t normally normalize for gene length (like we would with full length transcript bulk…

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TPM to logFC and pvalues

Hi, I assume you have to find differential expression between two cell lines (Cx and Dx groups). Since you need logFC and Pvalue, this R code can work. And you can use obtained matrix (mysample) to calculate FDR of your interest. mysample <- read.table(“./mymatrix.csv”, sep=”,”, header=TRUE) for(i in 2:nrow(mysample)) {…

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